RNA binding protein (RBP) chains in the Protein-RNA complexes was mapped to Pfam
doamin version 37.0 hosted from InterPro.
Table S4:
The Pfam domain present in PRDBv3.0.
| PDB IDa | Proteinb | RNAc | Proteind | RNAe | PDB Domainf | Domain Nameg | Domain IDh | UniProt Idi | Startj | Endk | B (Å)l | Categorym | Classn | Caseso |
| 1ASY (A:R) | S. cerevisiae aspartyl-tRNA synthetase | tRNA-Asp | 1EOV (A) | 2TRA (A) | 1ASY (A) | tRNA anti-codon | PF01336 | P04802 | 109 | 197 | 1377 | R | A | UU |
| 1ASY (A:R) | S. cerevisiae aspartyl-tRNA synthetase | tRNA-Asp | 1EOV (A) | 2TRA (A) | 1ASY (A) | tRNA-synt 2 | PF00152 | P04802 | 227 | 552 | 2062 | R | A | UU |
| 1AV6 (A:B) | Vaccinia virus cap-specific mRNA methyltransferase | M7G capped RNA | 1B42 (A) | 1AV6 (A) | PARP_regulatory | PF01358 | P07617 | 5 | 296 | 845 | R | D | UB | |
| 1B23 (P:R) | T. aquaticus EF-TU | E. coli tRNA-Cys | 1TUI (A) | 1U0B* (A) | 1B23 (P) | GTP_EFTU | PF00009 | Q01698 | 10 | 213 | 665 | F | A | UU |
| 1B23 (P:R) | T. aquaticus EF-TU | E. coli tRNA-Cys | 1TUI (A) | 1U0B* (A) | 1B23 (P) | GTP_EFTU_D2 | PF03144 | Q01698 | 236 | 306 | 584 | F | A | UU |
| 1B23 (P:R) | T. aquaticus EF-TU | E. coli tRNA-Cys | 1TUI (A) | 1U0B* (A) | 1B23 (P) | GTP_EFTU_D3 | PF03143 | Q01698 | 310 | 405 | 996 | F | A | UU |
| 1C0A (A:B) | E. coli aspartyl-tRNA synthetase | tRNA-Asp | 1EQR (A) | 1EFW* (C) | 1C0A (A) | tRNA_anti-codon | PF01336 | P21889 | 18 | 102 | 1362 | S | A | UU |
| 1C0A (A:B) | E. coli aspartyl-tRNA synthetase | tRNA-Asp | 1EQR (A) | 1EFW* (C) | 1C0A (A) | tRNA-synt_2 | PF00152 | P21889 | 117 | 558 | 2178 | S | A | UU |
| 1C0A (A:B) | E. coli aspartyl-tRNA synthetase | tRNA-Asp | 1EQR (A) | 1EFW* (C) | 1C0A (A) | GAD | PF02938 | P21889 | 307 | 406 | 219 | S | A | UU |
| 1C9S (L:W1-7) | G. stearothermophilus TRAP | ssRNA | 2EXT (A) | 1C9S (L) | TrpBP | PF02081 | Q9X6J6 | 3 | 71 | 1028 | R | D | UB | |
| 1CVJ (A:M) | H. sapiens poly(A)-binding protein | polyA | 4F25 (A) | 1CVJ (A) | RRM_1 | PF00076 | P11940 | 13 | 83 | 1332 | F | D | UB | |
| 1CVJ (A:M) | H. sapiens poly(A)-binding protein | polyA | 4F25 (A) | 1CVJ (A) | RRM_1 | PF00076 | P11940 | 101 | 168 | 888 | F | D | UB | |
| 1DFU (P:MN) | E. coli ribosomal protein L25 | 5s rRNA | 1B75 (A) | 364D (CB) | 1DFU (P) | Ribosomal_L25p | PF01386 | P68919 | 4 | 91 | 1671 | F | B | UU |
| 1F7U (A:B) | S. cerevisiae arginyl-tRNA synthetase | tRNA-Arg | 1BS2 (A) | 1F7U (A) | Arg_tRNA_synt_N | PF03485 | Q05506 | 33 | 114 | 1164 | S | A | UB | |
| 1F7U (A:B) | S. cerevisiae arginyl-tRNA synthetase | tRNA-Arg | 1BS2 (A) | 1F7U (A) | tRNA-synt_1d | PF00750 | Q05506 | 123 | 475 | 2503 | S | A | UB | |
| 1F7U (A:B) | S. cerevisiae arginyl-tRNA synthetase | tRNA-Arg | 1BS2 (A) | 1F7U (A) | DALR_1 | PF05746 | Q05506 | 489 | 607 | 1881 | S | A | UB | |
| 1FEU (A:BC) | T. thermophilus ribosomal protein L5 | 5s rRNA | 2J01 (Z) | 364D* (BC) | 1FEU (A) | Ribosomal_L25p | PF01386 | P56930 | 5 | 88 | 1532 | S | B | UU |
| 1FEU (A:BC) | T. thermophilus ribosomal protein L5 | 5s rRNA | 2J01 (Z) | 364D* (BC) | 1FEU (A) | Ribosomal_TL5_C | PF14693 | P56930 | 95 | 178 | 42 | S | B | UU |
| 1G1X (ABC:DE) | T. thermophilus ribosomal proteins S6, S15, S18 | 16S rRNA | 1CQM (A) | 1G1X (A) | Ribosomal_S6 | PF01250 | Q5SLP8 | 3 | 92 | 918 | R | B | UB | |
| 1G1X (ABC:DE) | T. thermophilus ribosomal proteins S6, S15, S18 | 16S rRNA | 1CQM (A) | 1G1X (B) | Ribosomal_S15 | PF00312 | Q5SJ76 | 8 | 88 | 2617 | R | B | UB | |
| 1G1X (ABC:DE) | T. thermophilus ribosomal proteins S6, S15, S18 | 16S rRNA | 1CQM (A) | 1G1X (C) | Ribosomal_S18 | PF01084 | Q5SLQ0 | 31 | 79 | 1110 | R | B | UB | |
| 1G2E (A:B) | H. sapiens RRM domain of the HuD protein | class II ARE fragment | 4EGL (A) | 1G2E (A) | RRM_1 | PF00076 | P26378 | 53 | 123 | 1476 | R | D | UB | |
| 1G2E (A:B) | H. sapiens RRM domain of the HuD protein | class II ARE fragment | 4EGL (A) | 1G2E (A) | RRM_1 | PF00076 | P26378 | 139 | 207 | 1021 | R | D | UB | |
| 1H3E (AA':B) | T. thermophilus tyrosyl-tRNA synthetase | tRNA-Tyr | 1H3F (AB) | 1H3E (A) | tRNA-synt_1b | PF00579 | P83453 | 33 | 302 | 1877 | F | A | UB | |
| 1H4S (AB:T) | T. thermophilus prolyl-tRNA synthetase | tRNA-Pro | 1HC7 (AB) | 1H4S (A) | tRNA-synt_2b | PF00587 | Q5SM28 | 94 | 273 | 802 | R | A | UB | |
| 1H4S (AB:T) | T. thermophilus prolyl-tRNA synthetase | tRNA-Pro | 1HC7 (AB) | 1H4S (A) | HGTP_anticodon | PF03129 | Q5SM28 | 289 | 384 | 0 | R | A | UB | |
| 1H4S (AB:T) | T. thermophilus prolyl-tRNA synthetase | tRNA-Pro | 1HC7 (AB) | 1H4S (A) | ProRS-C_1 | PF09180 | Q5SM28 | 410 | 477 | 0 | R | A | UB | |
| 1H4S (AB:T) | T. thermophilus prolyl-tRNA synthetase | tRNA-Pro | 1HC7 (AB) | 1H4S (B) | tRNA-synt_2b | PF00587 | Q5SM28 | 94 | 273 | 19 | R | A | UB | |
| 1H4S (AB:T) | T. thermophilus prolyl-tRNA synthetase | tRNA-Pro | 1HC7 (AB) | 1H4S (B) | HGTP_anticodon | PF03129 | Q5SM28 | 289 | 384 | 1550 | R | A | UB | |
| 1H4S (AB:T) | T. thermophilus prolyl-tRNA synthetase | tRNA-Pro | 1HC7 (AB) | 1H4S (B) | ProRS-C_1 | PF09180 | Q5SM28 | 410 | 477 | 0 | R | A | UB | |
| 1HQ1 (A:B) | E. coli SRP | 4.5S RNA domain IV | 1DUH (A) | 1HQ1 (A) | SRP_SPB | PF02978 | P0AGD7 | 328 | 427 | 0 | C | BU | ||
| 1J1U (AA':B) | M. jannaschii tyrosyl-tRNA synthetase | tRNA-Tyr | 1U7D (AB) | 1J1U (A) | tRNA-synt_1b | PF00579 | Q57834 | 24 | 300 | 2245 | R | A | UB | |
| 1JBS (A:C) | A. restrictus restrictocin | SRD RNA analogue | 1AQZ (A) | 1Q9A (A) | 1JBS (A) | Ribonuclease | PF00545 | P67876 | 38 | 175 | 1313 | R | D | UU |
| 1JID (A:B) | H. sapiens SRP19 | SRP RNA | 1D4R (A) | 1JID (A) | SRP19 | PF01922 | P09132 | 17 | 115 | 1262 | C | BU | ||
| 1K8W (A:B) | E. coli pseudouridine synthase B | T stem-loop RNA | 1R3F (A) | 1K8W (A) | TruB_N | PF01509 | P60340 | 33 | 180 | 2713 | R | D | UB | |
| 1K8W (A:B) | E. coli pseudouridine synthase B | T stem-loop RNA | 1R3F (A) | 1K8W (A) | TruB_C_2 | PF16198 | P60340 | 181 | 249 | 376 | R | D | UB | |
| 1K8W (A:B) | E. coli pseudouridine synthase B | T stem-loop RNA | 1R3F (A) | 1K8W (A) | TruB_C_2 | PF09157 | P60340 | 252 | 309 | 47 | R | D | UB | |
| 1KQ2 (ABHIKM:R) | S. aureus Hfq | 7-mer RNA | 1KQ1 (ABHIKM) | 1KQ2 (A) | Hfq | PF17209 | A0A0H3JV59 | 7 | 65 | 643 | R | D | UB | |
| 1KQ2 (ABHIKM:R) | S. aureus Hfq | 7-mer RNA | 1KQ1 (ABHIKM) | 1KQ2 (B) | Hfq | PF17209 | A0A0H3JV59 | 7 | 66 | 663 | R | D | UB | |
| 1KQ2 (ABHIKM:R) | S. aureus Hfq | 7-mer RNA | 1KQ1 (ABHIKM) | 1KQ2 (H) | Hfq | PF17209 | A0A0H3JV59 | 7 | 66 | 585 | R | D | UB | |
| 1KQ2 (ABHIKM:R) | S. aureus Hfq | 7-mer RNA | 1KQ1 (ABHIKM) | 1KQ2 (I) | Hfq | PF17209 | A0A0H3JV59 | 7 | 65 | 536 | R | D | UB | |
| 1KQ2 (ABHIKM:R) | S. aureus Hfq | 7-mer RNA | 1KQ1 (ABHIKM) | 1KQ2 (K) | Hfq | PF17209 | A0A0H3JV59 | 7 | 66 | 546 | R | D | UB | |
| 1KQ2 (ABHIKM:R) | S. aureus Hfq | 7-mer RNA | 1KQ1 (ABHIKM) | 1KQ2 (M) | Hfq | PF17209 | A0A0H3JV59 | 7 | 66 | 668 | R | D | UB | |
| 1LNG (A:B) | M. jannaschii SRP19 | 7S SRP RNA | 1Z43 (A) | 1LNG (A) | SRP19 | PF01922 | Q58440 | 2 | 86 | 2331 | D | BU | ||
| 1M5O (C:B) | H. sapiens U1 Snp A | hairpin ribozyme | 1OIA (A) | 1M5O (C) | RRM_1 | PF00076 | P09012 | 12 | 83 | 1383 | R | D | UB | |
| 1M8V (AM:O) | P. abyssi Sm | uridine heptamer | 1H64 (AM) | 1M8V (A) | LSM | PF01423 | Q9V0Y8 | 107 | 172 | 474 | R | D | UB | |
| 1M8V (AM:O) | P. abyssi Sm | uridine heptamer | 1H64 (AM) | 1M8V (M) | LSM | PF01423 | Q9V0Y8 | 607 | 672 | 533 | R | D | UB | |
| 1M8W (A:CE) | H. sapiens pumilio-homology domain | Nre1-19 RNA | 1M8Z (A) | 1M8W (A) | PUF | PF00806 | Q14671 | 852 | 886 | 0 | R | D | UB | |
| 1M8W (A:CE) | H. sapiens pumilio-homology domain | Nre1-19 RNA | 1M8Z (A) | 1M8W (A) | PUF | PF00806 | Q14671 | 889 | 922 | 200 | R | D | UB | |
| 1M8W (A:CE) | H. sapiens pumilio-homology domain | Nre1-19 RNA | 1M8Z (A) | 1M8W (A) | PUF | PF00806 | Q14671 | 924 | 957 | 404 | R | D | UB | |
| 1M8W (A:CE) | H. sapiens pumilio-homology domain | Nre1-19 RNA | 1M8Z (A) | 1M8W (A) | PUF | PF00806 | Q14671 | 960 | 992 | 267 | R | D | UB | |
| 1M8W (A:CE) | H. sapiens pumilio-homology domain | Nre1-19 RNA | 1M8Z (A) | 1M8W (A) | PUF | PF00806 | Q14671 | 996 | 1030 | 356 | R | D | UB | |
| 1M8W (A:CE) | H. sapiens pumilio-homology domain | Nre1-19 RNA | 1M8Z (A) | 1M8W (A) | PUF | PF00806 | Q14671 | 1032 | 1066 | 406 | R | D | UB | |
| 1M8W (A:CE) | H. sapiens pumilio-homology domain | Nre1-19 RNA | 1M8Z (A) | 1M8W (A) | PUF | PF00806 | Q14671 | 1068 | 1102 | 425 | R | D | UB | |
| 1M8W (A:CE) | H. sapiens pumilio-homology domain | Nre1-19 RNA | 1M8Z (A) | 1M8W (A) | PUF | PF00806 | Q14671 | 1112 | 1145 | 444 | R | D | UB | |
| 1MMS (A:C) | T. maritima ribosomal protein L11 | 23S rRNA fragment | 2K3F (A) | 3I9C* (A:1080-1129) | 1MMS (A) | Ribosomal_L11_N | PF03946 | P29395 | 9 | 66 | 416 | F | B | UU |
| 1MMS (A:C) | T. maritima ribosomal protein L11 | 23S rRNA fragment | 2K3F (A) | 3I9C* (A:1080-1129) | 1MMS (A) | Ribosomal_L11 | PF00298 | P29395 | 71 | 139 | 2072 | F | B | UU |
| 1MSW (D:R) | Phage T7 RNA polymerase | RNA transcript | 1ARO (P) | 1MSW (D) | RPOL_N | PF14700 | P00573 | 35 | 325 | 1621 | F | C | UB | |
| 1MSW (D:R) | Phage T7 RNA polymerase | RNA transcript | 1ARO (P) | 1MSW (D) | RNA_pol | PF00940 | P00573 | 450 | 862 | 2400 | F | C | UB | |
| 1N35 (A:BC) | Reovirus polymerase | dsRNA | 1MUK (A) | 1N35 (A) | RdRP_5 | PF07925 | P0CK31 | 2 | 1263 | 1738 | R | C | UB | |
| 1N78 (A:C) | T. thermophilus glutamyl-tRNA synthetase | tRNA-Glu | 1J09 (A) | 1N78 (A) | tRNA-synt_1c | PF00749 | P27000 | 1 | 312 | 3496 | R | A | UB | |
| 1N78 (A:C) | T. thermophilus glutamyl-tRNA synthetase | tRNA-Glu | 1J09 (A) | 1N78 (A) | Anticodon_2 | PF19269 | P27000 | 326 | 467 | 895 | R | A | UB | |
| 1OOA (A:C) | M. musculus NF-kappaB p50 | aptamer RNA | 1LE5 (B) | 2JWV* (A) | 1OOA (A) | RHD_DNA_bind | PF00554 | P25799 | 42 | 240 | 1496 | F | C | UU |
| 1OOA (A:C) | M. musculus NF-kappaB p50 | aptamer RNA | 1LE5 (B) | 2JWV* (A) | 1OOA (A) | RHD_dimer | PF16179 | P25799 | 249 | 350 | 131 | F | C | UU |
| 1Q2R (AB:E) | Z. mobilis guanine transglycosylase | 20-mer tRNA fragment | 1R5Y (AA') | 1Q2R (A) | TGT | PF01702 | P28720 | 21 | 383 | 2662 | S | C | UB | |
| 1Q2R (AB:E) | Z. mobilis guanine transglycosylase | 20-mer tRNA fragment | 1R5Y (AA') | 1Q2R (A) | TGT | PF01702 | P28720 | 21 | 382 | 0 | S | C | UB | |
| 1QF6 (A:B) | E. coli threonyl-tRNA synthetase | tRNA-Thr | 1EVL (A) | 1QF6 (A) | TGS | PF02824 | P0A8M3 | 2 | 61 | 0 | R | A | UB | |
| 1QF6 (A:B) | E. coli threonyl-tRNA synthetase | tRNA-Thr | 1EVL (A) | 1QF6 (A) | tRNA_SAD | PF07973 | P0A8M3 | 171 | 219 | 814 | R | A | UB | |
| 1QF6 (A:B) | E. coli threonyl-tRNA synthetase | tRNA-Thr | 1EVL (A) | 1QF6 (A) | tRNA-synt_2b | PF00587 | P0A8M3 | 318 | 529 | 1218 | R | A | UB | |
| 1QF6 (A:B) | E. coli threonyl-tRNA synthetase | tRNA-Thr | 1EVL (A) | 1QF6 (A) | HGTP_anticodon | PF03129 | P0A8M3 | 541 | 631 | 1556 | R | A | UB | |
| 1QTQ (A:B) | E. coli glutaminyl-tRNA synthetase | tRNA-Gln | 1NYL (A) | 3KNH* (Y) | 1QTQ (A) | tRNA-synt_1c | PF00749 | P00962 | 27 | 338 | 3620 | S | A | UU |
| 1QTQ (A:B) | E. coli glutaminyl-tRNA synthetase | tRNA-Gln | 1NYL (A) | 3KNH* (Y) | 1QTQ (A) | tRNA-synt_1c_C | PF03950 | P00962 | 340 | 439 | 854 | S | A | UU |
| 1QTQ (A:B) | E. coli glutaminyl-tRNA synthetase | tRNA-Gln | 1NYL (A) | 3KNH* (Y) | 1QTQ (A) | tRNA-synt_1c_C2 | PF20974 | P00962 | 456 | 528 | 314 | S | A | UU |
| 1R3E (A:C) | T. maritime pseudouridine synthase TruB | tRNA fragment | 1ZE1 (A) | 1EHZ (A:49-65) | 1R3E (A) | TruB_N | PF01509 | Q9WZW0 | 24 | 171 | 2975 | F | C | UU |
| 1R3E (A:C) | T. maritime pseudouridine synthase TruB | tRNA fragment | 1ZE1 (A) | 1EHZ (A:49-65) | 1R3E (A) | TruB_C_2 | PF16198 | Q9WZW0 | 172 | 227 | 604 | F | C | UU |
| 1R3E (A:C) | T. maritime pseudouridine synthase TruB | tRNA fragment | 1ZE1 (A) | 1EHZ (A:49-65) | 1R3E (A) | PUA | PF01472 | Q9WZW0 | 230 | 300 | 356 | F | C | UU |
| 1SDS (C:FF') | M. jannaschii 50S ribosomal protein L7Ae | box H/ACA sRNA | 1XBI (A) | 1SDS (C) | Ribosomal_L7Ae | PF01248 | P54066 | 12 | 106 | 1200 | R | B | UB | |
| 1SER (AB:T) | T. thermophilus seryl-tRNA synthetase | tRNA-Ser | 1SES (AB) | 1SER (A) | Seryl_tRNA_N | PF02403 | P34945 | 1 | 105 | 134 | S | A | UB | |
| 1SER (AB:T) | T. thermophilus seryl-tRNA synthetase | tRNA-Ser | 1SES (AB) | 1SER (A) | tRNA-synt_2b | PF00587 | P34945 | 213 | 395 | 245 | S | A | UB | |
| 1SER (AB:T) | T. thermophilus seryl-tRNA synthetase | tRNA-Ser | 1SES (AB) | 1SER (B) | Seryl_tRNA_N | PF02403 | P34945 | 1 | 105 | 1436 | S | A | UB | |
| 1SER (AB:T) | T. thermophilus seryl-tRNA synthetase | tRNA-Ser | 1SES (AB) | 1SER (B) | tRNA-synt_2b | PF00587 | P34945 | 213 | 395 | 279 | S | A | UB | |
| 1U0B (B:A) | E. coli cysteinyl-tRNA synthetase | tRNA-Cys | 1LI5 (B) | 1U0B (B) | tRNA-synt_1e | PF01406 | P21888 | 14 | 314 | 2636 | R | A | UB | |
| 1U0B (B:A) | E. coli cysteinyl-tRNA synthetase | tRNA-Cys | 1LI5 (B) | 1U0B (B) | DALR_2 | PF09190 | P21888 | 341 | 402 | 953 | R | A | UB | |
| 1UVI (A:D) | phi6 RNA polymerase | 6-mer RNA | 1HHS (A) | 1UVI (A) | RdRP_1 | PF00680 | P11124 | 35 | 607 | 1360 | R | D | UB | |
| 1VFG (B:D) | A. aeolicus CCA-adding enzyme | tRNA | 4WBY (A) | 1VFG (B) | PolyA_pol | PF01743 | O66728 | 454 | 580 | 0 | R | A | UB | |
| 1WNE (A:BC) | Foot-and-mouth disease virus polymerase | template-primer RNA deca | 1U09 (A) | 1WNE (A) | RdRP_1 | PF00680 | Q9QCE4 | 1879 | 2306 | 0 | R | C | UB | |
| 1WPU (A:C) | B. subtilis HutP antitermination protein | hut mRNA | 1WPV (A) | 1WPU (A) | HutP | PF09021 | P10943 | 9 | 146 | 1358 | R | D | UB | |
| 1WSU (A:E) | M. thermoacetica elongation factor SelB | SECIS RNA | 1LVA (A) | 2RLU (A) | 1WSU (A) | SelB-wing_3 | PF09107 | Q46455 | 585 | 631 | 938 | R | D | UU |
| 1YVP (B:EFH) | X. laevis Ro autoantigen | Y RNA | 1YVR (A) | 1YVP (B) | TROVE | PF05731 | P42700 | 16 | 330 | 3496 | R | C | UB | |
| 1ZBH (AD:E) | H. sapiens exonuclease ERI1 | histone mRNA | 1ZBU (AD) | 1JU7 (A) | 1ZBH (A) | SAP | PF02037 | Q8IV48 | 76 | 110 | 270 | R | D | UU |
| 1ZBH (AD:E) | H. sapiens exonuclease ERI1 | histone mRNA | 1ZBU (AD) | 1JU7 (A) | 1ZBH (A) | RNase_T | PF00929 | Q8IV48 | 131 | 306 | 595 | R | D | UU |
| 1ZBH (AD:E) | H. sapiens exonuclease ERI1 | histone mRNA | 1ZBU (AD) | 1JU7 (A) | 1ZBH (D) | SAP | PF02037 | Q8IV48 | 76 | 110 | 298 | R | D | UU |
| 1ZBH (AD:E) | H. sapiens exonuclease ERI1 | histone mRNA | 1ZBU (AD) | 1JU7 (A) | 1ZBH (D) | RNase_T | PF00929 | Q8IV48 | 131 | 306 | 627 | R | D | UU |
| 1ZBI (A:CD) | B. halodurans RNase H | A form RNA | 1ZBF (A) | 1ZBI (A) | Ribonuclease H | IPR002156 | Q9KEI9 | 4 | 142 | 1393 | R | C | UB | |
| 2A8V (B:E) | E. coli RHO | Cytosine rich RNA | 1A8V (B) | 2A8V (B) | Rho_N | PF07498 | P0AG30 | 5 | 47 | 0 | S | D | UB | |
| 2A8V (B:E) | E. coli RHO | Cytosine rich RNA | 1A8V (B) | 2A8V (B) | Rho_RNA_bind | PF07497 | P0AG30 | 51 | 118 | 719 | S | D | UB | |
| 2ASB (A:B) | M. tuberculosis Nus A antiterminator | BoxC rRNA | 1K0R (A) | 2ASB (A) | KH_5 | PF13184 | P9WIV3 | 214 | 282 | 986 | R | D | UB | |
| 2AZ0 (AB:CD) | Flock house virus B2 | siRNA | 2B9Z (AB) | 2AZ0 (A) | B2 | PF11473 | P68831 | 2 | 71 | 1294 | R | C | UB | |
| 2AZ0 (AB:CD) | Flock house virus B2 | siRNA | 2B9Z (AB) | 2AZ0 (B) | B2 | PF11473 | P68831 | 2 | 72 | 1325 | R | C | UB | |
| 2AZX (AA':C) | H. sapiens tryptophanyl-tRNA synthetase | tRNA-Trp | 1R6U (AB) | 2AZX (A) | tRNA-synt_1b | PF00579 | P23381 | 151 | 443 | 2058 | R | A | UB | |
| 2BGG (A:PQ) | A. fulgidus PIWI | siRNA | 1W9H (A) | 2BGG (A) | Piwi | PF02171 | O28951 | 110 | 406 | 1976 | R | C | UB | |
| 2BH2 (A:C) | E. coli methyltransferase RumA | 23S rRNA | 1UWV (A) | 1JZX* (A:1915-1951) | 2BH2 (A) | TRAM | PF01938 | P55135 | 15 | 67 | 1258 | R | D | UU |
| 2BTE (A:B) | T. thermophilus leucyl-tRNA synthetase | tRNA-Leu | 1OBC (A) | 2NQP* (F) | 2BTE (A) | tRNA-synt_1g | PF09334 | Q7SIE4 | 35 | 183 | 0 | R | A | UU |
| 2BTE (A:B) | T. thermophilus leucyl-tRNA synthetase | tRNA-Leu | 1OBC (A) | 2NQP* (F) | 2BTE (A) | tRNA-synt_1_2 | PF13603 | Q7SIE4 | 221 | 406 | 706 | R | A | UU |
| 2BTE (A:B) | T. thermophilus leucyl-tRNA synthetase | tRNA-Leu | 1OBC (A) | 2NQP* (F) | 2BTE (A) | tRNA-synt_1 | PF00133 | Q7SIE4 | 408 | 581 | 145 | R | A | UU |
| 2BTE (A:B) | T. thermophilus leucyl-tRNA synthetase | tRNA-Leu | 1OBC (A) | 2NQP* (F) | 2BTE (A) | Leucyl-specific | PF14795 | Q7SIE4 | 580 | 635 | 0 | R | A | UU |
| 2BTE (A:B) | T. thermophilus leucyl-tRNA synthetase | tRNA-Leu | 1OBC (A) | 2NQP* (F) | 2BTE (A) | Anticodon_1 | PF08264 | Q7SIE4 | 718 | 843 | 1138 | R | A | UU |
| 2DRB (A:B) | A. fulgidus CCA-adding enzyme | tRNAminiCCA | 1UET (A) | 3Q1Q* (C) | 2DRB (A) | NTP_transf_2 | PF01909 | O28126 | 25 | 133 | 911 | S | A | UU |
| 2DRB (A:B) | A. fulgidus CCA-adding enzyme | tRNAminiCCA | 1UET (A) | 3Q1Q* (C) | 2DRB (A) | tRNA_NucTransf2 | PF09249 | O28126 | 146 | 255 | 740 | S | A | UU |
| 2DRB (A:B) | A. fulgidus CCA-adding enzyme | tRNAminiCCA | 1UET (A) | 3Q1Q* (C) | 2DRB (A) | CAA_C | PF21133 | O28126 | 274 | 417 | 1799 | S | A | UU |
| 2EZ6 (AB:CD) | A. aeolicus RNase III | 28-mer RNA | 1JFZ (AB) | 2EZ6 (A) | Ribonuclease_3 | PF00636 | O67082 | 37 | 121 | 833 | R | C | UB | |
| 2EZ6 (AB:CD) | A. aeolicus RNase III | 28-mer RNA | 1JFZ (AB) | 2EZ6 (A) | dsrm | PF00035 | O67082 | 152 | 217 | 1638 | R | C | UB | |
| 2EZ6 (AB:CD) | A. aeolicus RNase III | 28-mer RNA | 1JFZ (AB) | 2EZ6 (B) | Ribonuclease_3 | PF00636 | O67082 | 37 | 121 | 816 | R | C | UB | |
| 2EZ6 (AB:CD) | A. aeolicus RNase III | 28-mer RNA | 1JFZ (AB) | 2EZ6 (B) | dsrm | PF00035 | O67082 | 152 | 217 | 1623 | R | C | UB | |
| 2F8S (AB:CD) | A. aeolicus argonaute | siRNA | 1YVU (A) | 2F8S (A) | Aa-Ago_N | PF22430 | O67434 | 19 | 88 | 7 | S | C | UB | |
| 2F8S (AB:CD) | A. aeolicus argonaute | siRNA | 1YVU (A) | 2F8S (A) | PAZ_4 | PF18349 | O67434 | 167 | 259 | 439 | S | C | UB | |
| 2F8S (AB:CD) | A. aeolicus argonaute | siRNA | 1YVU (A) | 2F8S (A) | Piwi | PF02171 | O67434 | 419 | 694 | 0 | S | C | UB | |
| 2F8S (AB:CD) | A. aeolicus argonaute | siRNA | 1YVU (A) | 2F8S (B) | Aa-Ago_N | PF22430 | O67434 | 19 | 88 | 0 | S | C | UB | |
| 2F8S (AB:CD) | A. aeolicus argonaute | siRNA | 1YVU (A) | 2F8S (B) | PAZ_4 | PF18349 | O67434 | 167 | 259 | 0 | S | C | UB | |
| 2F8S (AB:CD) | A. aeolicus argonaute | siRNA | 1YVU (A) | 2F8S (B) | Piwi | PF02171 | O67434 | 419 | 694 | 0 | S | C | UB | |
| 2FK6 (A:R) | B. subtilis RNase Z | tRNA-Thr | 1Y44 (A) | 2FK6 (A) | Lactamase_B_2 | PF12706 | P54548 | 33 | 157 | 681 | R | A | UB | |
| 2FK6 (A:R) | B. subtilis RNase Z | tRNA-Thr | 1Y44 (A) | 2FK6 (A) | Lactamase_B_2 | PF12706 | P54548 | 196 | 270 | 5 | R | A | UB | |
| 2FMT (A:C) | E. coli methionyl-tRNAfmet transformylase | tRNAfmet | 1FMT (A) | 3CW6 (A) | 2FMT (A) | Formyl_trans_N | PF00551 | P23882 | 5 | 184 | 1290 | R | A | UU |
| 2FMT (A:C) | E. coli methionyl-tRNAfmet transformylase | tRNAfmet | 1FMT (A) | 3CW6 (A) | 2FMT (A) | Formyl_trans_C | PF02911 | P23882 | 207 | 305 | 1664 | R | A | UU |
| 2GIC (A:R) | VSV nucleocapsid | viral genomic RNA | 2QVJ (A) | 2GIC (A) | Rhabdo_ncap | PF00945 | P03521 | 10 | 405 | 1681 | R | D | UB | |
| 2GJW (AB:EFH) | A. fulgidus splicing endonuclease | bulge-helix-bulge RNA | 1R0V (A) | 2GJW (A) | tRNA_int_endo_N | PF02778 | O29362 | 149 | 209 | 0 | R | C | UB | |
| 2GJW (AB:EFH) | A. fulgidus splicing endonuclease | bulge-helix-bulge RNA | 1R0V (A) | 2GJW (A) | tRNA_int_endo | PF01974 | O29362 | 216 | 299 | 1171 | R | C | UB | |
| 2GJW (AB:EFH) | A. fulgidus splicing endonuclease | bulge-helix-bulge RNA | 1R0V (B) | 2GJW (B) | tRNA_int_endo_N | PF02778 | O29362 | 149 | 209 | 84 | R | C | UB | |
| 2GJW (AB:EFH) | A. fulgidus splicing endonuclease | bulge-helix-bulge RNA | 1R0V (B) | 2GJW (B) | tRNA_int_endo | PF01974 | O29362 | 216 | 299 | 1352 | R | C | UB | |
| 2GXB (A:EF) | H. sapiens Z alpha domain of adenosine deaminase | dsRNA | 1QGP (A) | 2GXB (A) | z-alpha | PF02295 | P55265 | 140 | 198 | 769 | R | C | UB | |
| 2HW8 (A:B) | T. thermophilus ribosomal protein L1 | mRNA | 1AD2 (A) | 2HW8 (A) | Ribosomal_L1 | PF00687 | P27150 | 30 | 221 | 1922 | F | B | UB | |
| 2I82 (A:E) | E. coli pseudouridine synthase RluA | tRNA-Phe | 3L0U (A) | 2I82 (A) | PseudoU_synth_2 | PF00849 | P0AA37 | 22 | 170 | 2847 | D | BU | ||
| 2IX1 (A:B) | E. coli RNase II | polyA | 2IX0 (A) | 2IX1 (A) | OB_RNB | PF08206 | P30850 | 24 | 81 | 226 | R | D | UB | |
| 2IX1 (A:B) | E. coli RNase II | polyA | 2IX0 (A) | 2IX1 (A) | CSD2 | PF17876 | P30850 | 99 | 175 | 549 | R | D | UB | |
| 2IX1 (A:B) | E. coli RNase II | polyA | 2IX0 (A) | 2IX1 (A) | RNB | PF00773 | P30850 | 189 | 517 | 2185 | R | D | UB | |
| 2IX1 (A:B) | E. coli RNase II | polyA | 2IX0 (A) | 2IX1 (A) | S1 | PF00575 | P30850 | 557 | 636 | 817 | R | D | UB | |
| 2JEA (AB:C) | S. solfataricus exosome | substrate RNA | 2JE6 (AB) | 2JEA (A) | RNase_PH | PF01138 | Q9UXC0 | 36 | 171 | 566 | R | D | UB | |
| 2JEA (AB:C) | S. solfataricus exosome | substrate RNA | 2JE6 (AB) | 2JEA (A) | RNase_PH_C | PF03725 | Q9UXC0 | 195 | 261 | 0 | R | D | UB | |
| 2JEA (AB:C) | S. solfataricus exosome | substrate RNA | 2JE6 (AB) | 2JEA (B) | RNase_PH | PF01138 | Q9UXC2 | 27 | 156 | 846 | R | D | UB | |
| 2JEA (AB:C) | S. solfataricus exosome | substrate RNA | 2JE6 (AB) | 2JEA (B) | RNase_PH_C | PF03725 | Q9UXC2 | 159 | 224 | 304 | R | D | UB | |
| 2JLU (A:C) | Dengue virus serine protease subunit NS3 | ssRNA | 2JLQ (A) | 2JLU (A) | Flavi_DEAD | PF07652 | Q2YHF0 | 183 | 330 | 1030 | S | D | UB | |
| 2OZB (AB:C) | H. sapiens ribonucleoprotein | U4snRNA | 2XEB (AB) | 2OZB (A) | Ribosomal_L7Ae | PF01248 | P55769 | 20 | 114 | 1305 | S | C | UU | |
| 2OZB (AB:C) | H. sapiens ribonucleoprotein | U4snRNA | 2XEB (AB) | 2OZB (B) | Nop | PF01798 | Q8WWY3 | 99 | 330 | 1364 | S | C | UU | |
| 2PJP (A:B) | E. coli SelB | SECIS RNA | 1MFK (A) | 2PJP (A) | SelB_WH_2nd_bact | PF21214 | P14081 | 487 | 545 | 385 | C | BU | ||
| 2PJP (A:B) | E. coli SelB | SECIS RNA | 1MFK (A) | 2PJP (A) | SelB-wing_3 | PF09107 | P14081 | 559 | 605 | 944 | C | BU | ||
| 2PY9 (B:E) | H. sapiens poly(rC)-binding protein 2 | human telomeric RNA | 2JZX (A:1-73) | 2PY9 (B) | KH_1 | PF00013 | Q15366 | 15 | 77 | 1061 | R | D | UB | |
| 2Q66 (A:X) | S. cerevisiae poly(A) polymerase | polyA | 2HHP (A) | 2Q66 (A) | NTP_transf_2 | PF01909 | P29468 | 69 | 161 | 748 | S | D | UB | |
| 2Q66 (A:X) | S. cerevisiae poly(A) polymerase | polyA | 2HHP (A) | 2Q66 (A) | PAP_central | PF04928 | P29468 | 206 | 351 | 598 | S | D | UB | |
| 2Q66 (A:X) | S. cerevisiae poly(A) polymerase | polyA | 2HHP (A) | 2Q66 (A) | PAP_RNA-bind | PF04926 | P29468 | 353 | 529 | 591 | S | D | UB | |
| 2QUX (AB:C) | Pseudomonas phage PP7 coat protein | hairpin RNA | 2QUD (A) | 2QUX (A) | Phage_coat | PF09063 | P03630 | 2 | 127 | 867 | R | C | UB | |
| 2QUX (AB:C) | Pseudomonas phage PP7 coat protein | hairpin RNA | 2QUD (B) | 2QUX (B) | Phage_coat | PF09063 | P03630 | 2 | 127 | 1148 | R | C | UB | |
| 2R7R (A:X) | Rotavirus polymerase VP1 | RNA | 2R7Q (A) | 2Q66 (A) | RdRP_4 | PF02123 | O37061 | 100 | 748 | 0 | S | D | UB | |
| 2R7R (A:X) | Rotavirus polymerase VP1 | RNA | 2R7Q (A) | 2Q66 (A) | Rotavirus_VP1 | PF12289 | O37061 | 778 | 1088 | 215 | S | D | UB | |
| 2R8S (LH:R) | M. musculus synthetic FAB | ribozyme | 2HFF (AB) | 1HR2 (A) | 2R8S (H) | Ig C1-set | PF07654 | NA | 129 | 209 | 0 | S | C | UU |
| 2R8S (LH:R) | M. musculus synthetic FAB | ribozyme | 2HFF (AB) | 1HR2 (A) | 2R8S (H) | Ig V-set | PF07686 | NA | 12 | 119 | 1594 | S | C | UU |
| 2R8S (LH:R) | M. musculus synthetic FAB | ribozyme | 2HFF (AB) | 1HR2 (A) | 2R8S (L) | Ig C1-set | PF07654 | NA | 115 | 201 | 0 | S | C | UU |
| 2R8S (LH:R) | M. musculus synthetic FAB | ribozyme | 2HFF (AB) | 1HR2 (A) | 2R8S (L) | Ig V-set | PF07686 | NA | 6 | 106 | 1020 | S | C | UU |
| 2XGJ (A:C) | S. cerevisiae Mtr4 | polyA | 4U4C (A) | 2XGJ (A) | DEAD | PF00270 | P47047 | 151 | 302 | 463 | F | D | UB | |
| 2XGJ (A:C) | S. cerevisiae Mtr4 | polyA | 4U4C (A) | 2XGJ (A) | Helicase_C | PF00271 | P47047 | 436 | 548 | 516 | F | D | UB | |
| 2XGJ (A:C) | S. cerevisiae Mtr4 | polyA | 4U4C (A) | 2XGJ (A) | MTR4-like_stalk | PF21408 | P47047 | 602 | 665 | 0 | F | D | UB | |
| 2XGJ (A:C) | S. cerevisiae Mtr4 | polyA | 4U4C (A) | 2XGJ (A) | MTR4_beta-barrel | PF13234 | P47047 | 666 | 872 | 0 | F | D | UB | |
| 2XGJ (A:C) | S. cerevisiae Mtr4 | polyA | 4U4C (A) | 2XGJ (A) | DSHCT | PF08148 | P47047 | 898 | 1068 | 268 | F | D | UB | |
| 2XNR (A:C) | S. cerevisiae Nab3-RRM | UCUU recognition sequen | 2XNQ (A) | 2XNR (A) | RRM_1 | PF00076 | P38996 | 332 | 395 | 695 | R | D | UB | |
| 2XZO (A:D) | H. sapiens Upf1 helicase | polyU | 2XZP (A) | 2XZO (A) | UPF1_1B_dom | PF18141 | Q92900 | 324 | 425 | 301 | F | D | UB | |
| 2XZO (A:D) | H. sapiens Upf1 helicase | polyU | 2XZP (A) | 2XZO (A) | AAA_11 | PF13086 | Q92900 | 481 | 605 | 413 | F | D | UB | |
| 2XZO (A:D) | H. sapiens Upf1 helicase | polyU | 2XZP (A) | 2XZO (A) | AAA_11 | PF13086 | Q92900 | 579 | 684 | 621 | F | D | UB | |
| 2XZO (A:D) | H. sapiens Upf1 helicase | polyU | 2XZP (A) | 2XZO (A) | AAA_12 | PF13087 | Q92900 | 691 | 888 | 735 | F | D | UB | |
| 2Y8W (A:B) | T. thermophilus endoribonuclease Cse3 | hairpin RNA | 1WJ9 (A) | 2Y8W (A) | CRISPR_assoc | PF08798 | Q53WG9 | 1 | 211 | 3258 | F | C | UB | |
| 2YKG (A:CD) | H. sapiens RIG-I | dsRNA | 4QI0 (A) | 2YKG (A) | DEAD | PF00270 | O95786 | 244 | 420 | 851 | R | C | UB | |
| 2YKG (A:CD) | H. sapiens RIG-I | dsRNA | 4QI0 (A) | 2YKG (A) | RIG-I_C | PF18119 | O95786 | 457 | 602 | 343 | R | C | UB | |
| 2YKG (A:CD) | H. sapiens RIG-I | dsRNA | 4QI0 (A) | 2YKG (A) | Helicase_C | PF00271 | O95786 | 609 | 734 | 0 | R | C | UB | |
| 2YKG (A:CD) | H. sapiens RIG-I | dsRNA | 4QI0 (A) | 2YKG (A) | RIG-I_C-RD | PF11648 | O95786 | 806 | 922 | 914 | R | C | UB | |
| 2ZKO (AB:CD) | NS1 protein of influenza A | A-form dsRNA | 2Z0A (A) | 2ZKO (A) | Flu_NS1 | PF00600 | P03496 | 1 | 70 | 1290 | R | C | UB | |
| 2ZKO (AB:CD) | NS1 protein of influenza A | A-form dsRNA | 2Z0A (B) | 2ZKO (B) | Flu_NS1 | PF00600 | P03496 | 1 | 70 | 1273 | R | C | UB | |
| 2ZM5 (A:C) | E. coli iso-pent-enyl-transferase | tRNA-Phe | 3L0U (A) | 2ZM5 (A) | IPPT | PF01715 | P16384 | 45 | 289 | 3866 | A | BU | ||
| 2ZZM (A:B) | M. jannaschii tRNA (guanine(37)-N1)-methyltransferas | tRNA-Leu | 2YX1 (A) | 1WZ2* (C) | 2ZZM (A) | Trm5_N | PF18093 | Q58293 | 4 | 51 | 1069 | F | A | UU |
| 3A6P (AC:DE) | H. sapiens exp-5:RanGTP | pre-microRNA | 5YU7:A | 3A6P (A) | IBN_N | PF03810 | Q9HAV4 | 33 | 100 | 0 | S | C | UB | |
| 3A6P (AC:DE) | H. sapiens exp-5:RanGTP | pre-microRNA | 5YU7:A | 3A6P (A) | Xpo1 | PF08389 | Q9HAV4 | 109 | 271 | 0 | S | C | UB | |
| 3A6P (AC:DE) | H. sapiens exp-5:RanGTP | pre-microRNA | 5YU7:A | 3A6P (A) | Exportin-5 | PF19273 | Q9HAV4 | 313 | 1136 | 706 | S | C | UB | |
| 3A6P (AC:DE) | H. sapiens exp-5:RanGTP | pre-microRNA | 5YU7:A | 3A6P (C) | Ras | PF00071 | P62825 | 12 | 170 | 146 | S | C | UB | |
| 3ADB (A:C) | M. jannaschii O-phosphoseryl-tRNA kinase | tRNA-Sec | 3A4M (A) | 3ADB (A) | KTI12 | PF08433 | Q58933 | 1 | 246 | 3099 | F | A | UB | |
| 3AEV (B:C) | P. horikoshii Dim2p | P. horikoshii 16S rRNA fra | 2E3U (A) | 3AEV (B) | KH_1 | PF00013 | O59282 | 35 | 98 | 1038 | R | D | UB | |
| 3AEV (B:C) | P. horikoshii Dim2p | P. horikoshii 16S rRNA fra | 2E3U (A) | 3AEV (B) | KH_1 | PF00013 | O59282 | 128 | 187 | 1115 | R | D | UB | |
| 3AMT (A:B) | A. fulgidus agmatinylcytidine synthetase TiaS | tRNA-Ile | 3AU7 (A) | 3AMT (A) | TiaS-FLD | PF22641 | O28025 | 4 | 137 | 399 | R | A | UB | |
| 3AMT (A:B) | A. fulgidus agmatinylcytidine synthetase TiaS | tRNA-Ile | 3AU7 (A) | 3AMT (A) | DUF1743 | PF08489 | O28025 | 139 | 251 | 590 | R | A | UB | |
| 3AMT (A:B) | A. fulgidus agmatinylcytidine synthetase TiaS | tRNA-Ile | 3AU7 (A) | 3AMT (A) | tRNA_anti-codon | PF01336 | O28025 | 267 | 340 | 1625 | R | A | UB | |
| 3BSN (A:PT) | Norwalk virus polymerase | synthetic RNA | 1SH3 (A) | 3BSN (A) | RdRP_1 | PF00680 | Q70ET3 | 357 | 794 | 989 | S | C | UB | |
| 3BT7 (A:C) | E. coli methyltransferase TrmA | T-arm analogue | 1EVV (A) | 3BT7 (A) | tRNA_U5-meth_tr | PF05958 | P23003 | 10 | 366 | 2163 | C | BU | ||
| 3BX2 (A:C) | S. cerevisiae PUF4 | 3' UTR binding sequence | 3BWT (A) | 3BX2 (A) | PUF | PF00806 | P25339 | 567 | 600 | 265 | R | D | UB | |
| 3BX2 (A:C) | S. cerevisiae PUF4 | 3' UTR binding sequence | 3BWT (A) | 3BX2 (A) | PUF | PF00806 | P25339 | 603 | 635 | 409 | R | D | UB | |
| 3BX2 (A:C) | S. cerevisiae PUF4 | 3' UTR binding sequence | 3BWT (A) | 3BX2 (A) | PUF | PF00806 | P25339 | 639 | 673 | 439 | R | D | UB | |
| 3BX2 (A:C) | S. cerevisiae PUF4 | 3' UTR binding sequence | 3BWT (A) | 3BX2 (A) | PUF | PF00806 | P25339 | 676 | 710 | 279 | R | D | UB | |
| 3BX2 (A:C) | S. cerevisiae PUF4 | 3' UTR binding sequence | 3BWT (A) | 3BX2 (A) | PUF | PF00806 | P25339 | 712 | 746 | 267 | R | D | UB | |
| 3BX2 (A:C) | S. cerevisiae PUF4 | 3' UTR binding sequence | 3BWT (A) | 3BX2 (A) | PUF | PF00806 | P25339 | 749 | 774 | 378 | R | D | UB | |
| 3BX2 (A:C) | S. cerevisiae PUF4 | 3' UTR binding sequence | 3BWT (A) | 3BX2 (A) | PUF | PF00806 | P25339 | 788 | 818 | 408 | R | D | UB | |
| 3BX2 (A:C) | S. cerevisiae PUF4 | 3' UTR binding sequence | 3BWT (A) | 3BX2 (A) | PUF | PF00806 | P25339 | 828 | 859 | 437 | R | D | UB | |
| 3D2S (A:E) | H. sapiens MBNL1 ZnF3/4 | pre-mRNA | 3D2Q (A) | 3D2S (A) | zf-CCCH | PF00642 | Q9NR56 | 180 | 206 | 673 | R | D | UB | |
| 3D2S (A:E) | H. sapiens MBNL1 ZnF3/4 | pre-mRNA | 3D2Q (A) | 3D2S (A) | zf-CCCH_2 | PF14608 | Q9NR56 | 216 | 245 | 649 | R | D | UB | |
| 3DD2 (H:B) | H. sapiens thrombin | 26-mer RNA | 1JOU (D) | 3DD2 (H) | Trypsin | PF00089 | P00734 | 364 | 613 | 0 | R | C | UB | |
| 3EQT (AB:CD) | H. sapiens helicase DHX58 | dsRNA | 2W4R (A) | 3EQT (A) | RIG-I_C-RD | PF11648 | Q96C10 | 552 | 667 | 1381 | R | C | UB | |
| 3EQT (AB:CD) | H. sapiens helicase DHX58 | dsRNA | 2W4R (B) | 3EQT (B) | RIG-I_C-RD | PF11648 | Q96C10 | 552 | 667 | 1365 | R | C | UB | |
| 3FTE (A:CD) | A. aeolicus methyltransferase KsgA | rRNA | 3FTD (A) | 3FTE (A) | RrnaAD | PF00398 | O67680 | 14 | 245 | 837 | R | C | UB | |
| 3HL2 (AA'BB':E) | H. sapiens selenium transferase | tRNA-Sec | 3BC8 (AA'A''A''') | 3RG5 (A) | 3HL2 (A) | Trm5_N | PF18093 | Q58293 | 4 | 51 | 1069 | R | A | UU |
| 3IEV (A:D) | A. aeolicus GTPase era | 16S rRNA | 7C1O:A | 1SDR (B) | 3IEV (A) | MMR_HSR1 | PF01926 | O67800 | 5 | 124 | 0 | R | B | UU |
| 3KS8 (AB:EF) | R. ebolavirus polymerase cofactor VP35 | dsRNA | 3KS4 (A) | 3KS8 (A) | Filo_VP35 | PF02097 | Q8JPY0 | 208 | 329 | 1050 | R | C | UB | |
| 3KS8 (AB:EF) | R. ebolavirus polymerase cofactor VP35 | dsRNA | 3KS4 (B) | 3KS8 (B) | Filo_VP35 | PF02097 | Q8JPY0 | 206 | 329 | 682 | R | C | UB | |
| 3MDG (AB:C) | H. sapiens CFI(m)25 | pre-mRNA | 3BAP (AA') | 3BAP (A) | NUDIX_2 | PF13869 | O43809 | 35 | 222 | 1069 | R | D | UB | |
| 3MDG (AB:C) | H. sapiens CFI(m)25 | pre-mRNA | 3BAP (AA') | 3BAP (B) | NUDIX_2 | PF13869 | O43809 | 35 | 222 | 0 | R | D | UB | |
| 3MOJ (B:A) | B. subtilis helicase dbpA | E. coli 23S rRNA fragment | 2G0C (A) | 3MOJ (B) | DbpA | PF03880 | P42305 | 405 | 476 | 1759 | R | C | UB | |
| 3NMR (A:B) | H. sapiens CUG-binding protein 1 | UGU-rich mRNA | 2DHS (A) | 3NMR (A) | RRM_1 | PF00076 | Q92879 | 18 | 88 | 0 | S | D | UB | |
| 3NMR (A:B) | H. sapiens CUG-binding protein 1 | UGU-rich mRNA | 2DHS (A) | 3NMR (A) | RRM_1 | PF00076 | Q92879 | 110 | 178 | 879 | S | D | UB | |
| 3O3I (X:A) | H. sapiens Hiwi1 PAZ domain | piRNA | 2L5C (A) | 3O3I (X) | PAZ | PF02170 | Q96J94 | 280 | 393 | 923 | S | C | UB | |
| 3O8C (A:C) | HCV NS3 helicase | polyU | 3O8B (A) | 3O8C (A) | Flavi_DEAD | PF07652 | Q99AU2 | 30 | 178 | 0 | R | D | UB | |
| 3O8C (A:C) | HCV NS3 helicase | polyU | 3O8B (A) | 3O8C (A) | Peptidase_S29 | PF02907 | Q99AU2 | 255 | 336 | 514 | R | D | UB | |
| 3OIJ (AB:C) | S. cerevisiae methyltransferase | SSU rRNA | 3OII (A) | 3OIJ (A) | EMG1 | PF03587 | Q06287 | 43 | 246 | 1489 | S | C | UB | |
| 3OIJ (AB:C) | S. cerevisiae methyltransferase | SSU rRNA | 3OII (B) | 3OIJ (B) | EMG1 | PF03587 | Q06287 | 43 | 246 | 730 | S | C | UB | |
| 3OL6 (A:BCD) | Poliovirus polymerase | synthetic RNA | 1RA6 (A) | 3OL6 (A) | RdRP_1 | PF00680 | B3VQP5 | 1774 | 2187 | 0 | R | C | UB | |
| 3PF4 (B:R) | B. subtilis CspB | ssRNA | 1CSP (A) | 3PF4 (B) | CSD | PF00313 | P32081 | 2 | 66 | 893 | R | D | UB | |
| 3QJJ (A:Q) | P. horikoshii RAMP Protein | CRISPR repeat RNA | 3UFC (X) | 3QJJ (A) | Cas6_I-A | PF21350 | O58088 | 15 | 113 | 1149 | R | D | UB | |
| 3QJJ (A:Q) | P. horikoshii RAMP Protein | CRISPR repeat RNA | 3UFC (X) | 3QJJ (A) | Cas_Cas6_C | PF01881 | O58088 | 114 | 237 | 2175 | R | D | UB | |
| 3RC8 (A:E) | H. sapiens helicase SUPV3L1 | RNA fragment | 3RC3 (A) | 3RC8 (A) | Suv3_N | PF18114 | Q8IYB8 | 62 | 179 | 0 | R | D | UB | |
| 3RC8 (A:E) | H. sapiens helicase SUPV3L1 | RNA fragment | 3RC3 (A) | 3RC8 (A) | DEXQc_Suv3 | PF22527 | Q8IYB8 | 188 | 345 | 504 | R | D | UB | |
| 3RC8 (A:E) | H. sapiens helicase SUPV3L1 | RNA fragment | 3RC3 (A) | 3RC8 (A) | Helicase_C | PF00271 | Q8IYB8 | 351 | 475 | 615 | R | D | UB | |
| 3RC8 (A:E) | H. sapiens helicase SUPV3L1 | RNA fragment | 3RC3 (A) | 3RC8 (A) | Suv3_C_1 | PF18147 | Q8IYB8 | 556 | 598 | 328 | R | D | UB | |
| 3RC8 (A:E) | H. sapiens helicase SUPV3L1 | RNA fragment | 3RC3 (A) | 3RC8 (A) | SUV3_C | PF12513 | Q8IYB8 | 625 | 672 | 50 | R | D | UB | |
| 3RW6 (A:H) | H. sapiens nuclear RNA export factor 1 | CTE RNA | 3RW7 (A) | 3RW6 (A) | Tap-RNA_bind | PF09162 | Q9UBU9 | 119 | 198 | 1414 | F | C | UB | |
| 3SNP (A:C) | O. cuniculus iron regulatory protein 1 | ferritin H IRE RNA | 2B3Y (A) | 1AQO* (A) | 3SNP (A) | Aconitase | PF00330 | Q01059 | 59 | 564 | 1549 | F | C | UU |
| 3SNP (A:C) | O. cuniculus iron regulatory protein 1 | ferritin H IRE RNA | 2B3Y (A) | 1AQO* (A) | 3SNP (A) | Aconitase_C | PF00694 | Q01059 | 692 | 821 | 916 | F | C | UU |
| 3VJR (A:B) | E. coli peptidyl-tRNA hydrolase | tRNA CCA-acceptor | 2PTH (A) | INJM* (5) | 3VJR (A) | Pept_tRNA_hydro | PF01195 | P0A7D1 | 5 | 189 | 1256 | R | A | UU |
| 3ZC0 (AA'BB'CC'D | A. fulgidus C3PO | duplex RNA | 3ZC1:ABCDEFGH | 3ZC0 (A) | Translin | PF01997 | O28024 | 2 | 179 | 979 | R | C | UB | |
| 3ZC0 (AA'BB'CC'D | A. fulgidus C3PO | duplex RNA | 3ZC1:ABCDEFGH | 3ZC0 (B) | Translin | PF01997 | O28024 | 2 | 179 | 354 | R | C | UB | |
| 3ZC0 (AA'BB'CC'D | A. fulgidus C3PO | duplex RNA | 3ZC1:ABCDEFGH | 3ZC0 (C) | Translin | PF01997 | O28024 | 2 | 179 | 0 | R | C | UB | |
| 3ZC0 (AA'BB'CC'D | A. fulgidus C3PO | duplex RNA | 3ZC1:ABCDEFGH | 3ZC0 (D) | Translin | PF01997 | O28024 | 2 | 179 | 0 | R | C | UB | |
| 3ZC0 (AA'BB'CC'D | A. fulgidus C3PO | duplex RNA | 3ZC1:ABCDEFGH | 3ZC0 (E) | Translin | PF01997 | O28024 | 2 | 179 | 979 | R | C | UB | |
| 3ZC0 (AA'BB'CC'D | A. fulgidus C3PO | duplex RNA | 3ZC1:ABCDEFGH | 3ZC0 (F) | Translin | PF01997 | O28024 | 2 | 179 | 354 | R | C | UB | |
| 3ZC0 (AA'BB'CC'D | A. fulgidus C3PO | duplex RNA | 3ZC1:ABCDEFGH | 3ZC0 (G) | Translin | PF01997 | O28024 | 2 | 179 | 0 | R | C | UB | |
| 3ZC0 (AA'BB'CC'D | A. fulgidus C3PO | duplex RNA | 3ZC1:ABCDEFGH | 3ZC0 (H) | Translin | PF01997 | O28024 | 2 | 179 | 0 | R | C | UB | |
| 3ZJT (A:B) | E. coli leucyl-tRNA synthetase | tRNA-Leu | 2NQP (F) | 3ZJT (A) | tRNA-synt_1g | PF09334 | P07813 | 35 | 190 | 0 | A | BU | ||
| 3ZJT (A:B) | E. coli leucyl-tRNA synthetase | tRNA-Leu | 2NQP (F) | 3ZJT (A) | tRNA-synt_1_2 | PF13603 | P07813 | 221 | 404 | 603 | A | BU | ||
| 3ZJT (A:B) | E. coli leucyl-tRNA synthetase | tRNA-Leu | 2NQP (F) | 3ZJT (A) | tRNA-synt_1 | PF00133 | P07813 | 411 | 592 | 307 | A | BU | ||
| 3ZJT (A:B) | E. coli leucyl-tRNA synthetase | tRNA-Leu | 2NQP (F) | 3ZJT (A) | tRNA-synt_1 | PF00133 | P07813 | 609 | 659 | 472 | A | BU | ||
| 3ZJT (A:B) | E. coli leucyl-tRNA synthetase | tRNA-Leu | 2NQP (F) | 3ZJT (A) | Anticodon_1 | PF08264 | P07813 | 698 | 826 | 1446 | A | BU | ||
| 4E78 (A:PT) | HCV polymerase | RNA primer-template pair | 4E76 (A) | 4E78 (A) | RdRP_3 | PF00998 | Q99IB8 | 3 | 514 | 1675 | R | D | UB | |
| 4ERD (AB:CD) | T. thermophila p65 C-terminal domain | stem IV of telomerase RN | 4EYT (A) | 4ERD (A) | HTH La-type RNA-bi | PS50961 | W7X6T2 | 112 | 239 | 0 | R | C | UB | |
| 4ERD (AB:CD) | T. thermophila p65 C-terminal domain | stem IV of telomerase RN | 4EYT (A) | 4ERD (A) | RRM | PS50102 | W7X6T2 | 247 | 335 | 0 | R | C | UB | |
| 4ERD (AB:CD) | T. thermophila p65 C-terminal domain | stem IV of telomerase RN | 4EYT (A) | 4ERD (A) | xRRM | PS51939 | W7X6T2 | 374 | 542 | 1605 | R | C | UB | |
| 4FVU (A:BC) | Lassa virus exonuclease | dsRNA | 3Q7C (A) | 4FVU (A) | Arena_ncap_C | PF17290 | P13699 | 363 | 543 | 1240 | R | C | UB | |
| 4H5P (AB:E) | Rift valley fever virus nucleocapsid | polyU | 3LYF (AB) | 4H5P (A) | Tenui_N | PF05733 | D3K5I7 | 3 | 223 | 2342 | S | D | UB | |
| 4H5P (AB:E) | Rift valley fever virus nucleocapsid | polyU | 3LYF (AB) | 4H5P (B) | Tenui_N | PF05733 | D3K5I7 | 3 | 223 | 2325 | S | D | UB | |
| 4HOR (A:X) | H. sapiens IFIT | polyC | 4HOQ (A) | 4HOR (A) | TPR_12 | PF13424 | Q13325 | 49 | 117 | 0 | S | D | UB | |
| 4HOR (A:X) | H. sapiens IFIT | polyC | 4HOQ (A) | 4HOR (A) | TPR_8 | PF13181 | Q13325 | 147 | 173 | 0 | S | D | UB | |
| 4HOR (A:X) | H. sapiens IFIT | polyC | 4HOQ (A) | 4HOR (A) | TPR_10 | PF13374 | Q13325 | 340 | 368 | 90 | S | D | UB | |
| 4IG8 (A:BC) | H. sapiens oligoadenylate synthetase 1 | dsRNA | 1PX5 (A) | 4IG8 (A) | NTP_transf_2 | PF01909 | P00973 | 37 | 134 | 1094 | S | C | UB | |
| 4IG8 (A:BC) | H. sapiens oligoadenylate synthetase 1 | dsRNA | 1PX5 (A) | 4IG8 (A) | OAS1_C | PF10421 | P00973 | 163 | 346 | 901 | S | C | UB | |
| 4ILL (AB:RC) | S. solfataricus endoribonuclease Cas6 | CRISPR RNA | 4ILR (AA') | 4ILL (A) | Cas6_N | PF17952 | Q97WV8 | 5 | 120 | 1342 | R | C | UB | |
| 4ILL (AB:RC) | S. solfataricus endoribonuclease Cas6 | CRISPR RNA | 4ILR (AA') | 4ILL (A) | CRISPR_Cas6 | PF10040 | Q97WV8 | 5 | 120 | 1342 | R | C | UB | |
| 4ILL (AB:RC) | S. solfataricus endoribonuclease Cas6 | CRISPR RNA | 4ILR (AA') | 4ILL (B) | Cas6_N | PF17952 | Q97WV8 | 5 | 120 | 919 | R | C | UB | |
| 4ILL (AB:RC) | S. solfataricus endoribonuclease Cas6 | CRISPR RNA | 4ILR (AA') | 4ILL (B) | CRISPR_Cas6 | PF10040 | Q97WV8 | 139 | 277 | 2572 | R | C | UB | |
| 4J7M (A:B) | M. musculus Dom3Z | polyU | 4J7N (A) | 4J7M (A) | RAI1 | PF08652 | O70348 | 44 | 379 | 848 | R | D | UB | |
| 4M59 (AB:CD) | Z. mays chloroplast ppr10 | psaJ RNA | 4M57 (AA') | 4M59 (A) | PPR_3 | PF13812 | B8Y6I0 | 168 | 222 | 796 | F | D | UB | |
| 4M59 (AB:CD) | Z. mays chloroplast ppr10 | psaJ RNA | 4M57 (AA') | 4M59 (A) | PPR_1 | PF12854 | B8Y6I0 | 239 | 272 | 520 | F | D | UB | |
| 4M59 (AB:CD) | Z. mays chloroplast ppr10 | psaJ RNA | 4M57 (AA') | 4M59 (A) | PPR_2 | PF13041 | B8Y6I0 | 278 | 324 | 603 | F | D | UB | |
| 4M59 (AB:CD) | Z. mays chloroplast ppr10 | psaJ RNA | 4M57 (AA') | 4M59 (A) | PPR_2 | PF13041 | B8Y6I0 | 316 | 360 | 293 | F | D | UB | |
| 4M59 (AB:CD) | Z. mays chloroplast ppr10 | psaJ RNA | 4M57 (AA') | 4M59 (A) | PPR_2 | PF13041 | B8Y6I0 | 348 | 397 | 1 | F | D | UB | |
| 4M59 (AB:CD) | Z. mays chloroplast ppr10 | psaJ RNA | 4M57 (AA') | 4M59 (A) | PPR_2 | PF13041 | B8Y6I0 | 383 | 432 | 175 | F | D | UB | |
| 4M59 (AB:CD) | Z. mays chloroplast ppr10 | psaJ RNA | 4M57 (AA') | 4M59 (A) | PPR | PF01535 | B8Y6I0 | 456 | 486 | 110 | F | D | UB | |
| 4M59 (AB:CD) | Z. mays chloroplast ppr10 | psaJ RNA | 4M57 (AA') | 4M59 (A) | PPR_2 | PF13041 | B8Y6I0 | 488 | 537 | 143 | F | D | UB | |
| 4M59 (AB:CD) | Z. mays chloroplast ppr10 | psaJ RNA | 4M57 (AA') | 4M59 (A) | PPR_2 | PF13041 | B8Y6I0 | 594 | 643 | 702 | F | D | UB | |
| 4M59 (AB:CD) | Z. mays chloroplast ppr10 | psaJ RNA | 4M57 (AA') | 4M59 (A) | PPR_1 | PF12854 | B8Y6I0 | 661 | 694 | 486 | F | D | UB | |
| 4M59 (AB:CD) | Z. mays chloroplast ppr10 | psaJ RNA | 4M57 (AA') | 4M59 (A) | PPR | PF01535 | B8Y6I0 | 703 | 733 | 465 | F | D | UB | |
| 4M59 (AB:CD) | Z. mays chloroplast ppr10 | psaJ RNA | 4M57 (AA') | 4M59 (A) | PPR | PF01535 | B8Y6I0 | 738 | 763 | 250 | F | D | UB | |
| 4M59 (AB:CD) | Z. mays chloroplast ppr10 | psaJ RNA | 4M57 (AA') | 4M59 (B) | PPR_3 | PF13812 | B8Y6I0 | 168 | 222 | 812 | F | D | UB | |
| 4M59 (AB:CD) | Z. mays chloroplast ppr10 | psaJ RNA | 4M57 (AA') | 4M59 (B) | PPR_1 | PF12854 | B8Y6I0 | 239 | 272 | 511 | F | D | UB | |
| 4M59 (AB:CD) | Z. mays chloroplast ppr10 | psaJ RNA | 4M57 (AA') | 4M59 (B) | PPR_2 | PF13041 | B8Y6I0 | 278 | 327 | 568 | F | D | UB | |
| 4M59 (AB:CD) | Z. mays chloroplast ppr10 | psaJ RNA | 4M57 (AA') | 4M59 (B) | PPR_2 | PF13041 | B8Y6I0 | 316 | 360 | 258 | F | D | UB | |
| 4M59 (AB:CD) | Z. mays chloroplast ppr10 | psaJ RNA | 4M57 (AA') | 4M59 (B) | PPR_2 | PF13041 | B8Y6I0 | 350 | 397 | 0 | F | D | UB | |
| 4M59 (AB:CD) | Z. mays chloroplast ppr10 | psaJ RNA | 4M57 (AA') | 4M59 (B) | PPR_2 | PF13041 | B8Y6I0 | 383 | 432 | 76 | F | D | UB | |
| 4M59 (AB:CD) | Z. mays chloroplast ppr10 | psaJ RNA | 4M57 (AA') | 4M59 (B) | PPR | PF01535 | B8Y6I0 | 456 | 486 | 0 | F | D | UB | |
| 4M59 (AB:CD) | Z. mays chloroplast ppr10 | psaJ RNA | 4M57 (AA') | 4M59 (B) | PPR_2 | PF13041 | B8Y6I0 | 488 | 537 | 77 | F | D | UB | |
| 4M59 (AB:CD) | Z. mays chloroplast ppr10 | psaJ RNA | 4M57 (AA') | 4M59 (B) | PPR_2 | PF13041 | B8Y6I0 | 594 | 643 | 651 | F | D | UB | |
| 4M59 (AB:CD) | Z. mays chloroplast ppr10 | psaJ RNA | 4M57 (AA') | 4M59 (B) | PPR_1 | PF12854 | B8Y6I0 | 661 | 694 | 494 | F | D | UB | |
| 4M59 (AB:CD) | Z. mays chloroplast ppr10 | psaJ RNA | 4M57 (AA') | 4M59 (B) | PPR | PF01535 | B8Y6I0 | 703 | 733 | 448 | F | D | UB | |
| 4M59 (AB:CD) | Z. mays chloroplast ppr10 | psaJ RNA | 4M57 (AA') | 4M59 (B) | PPR | PF01535 | B8Y6I0 | 738 | 760 | 236 | F | D | UB | |
| 4MDX (AB:C) | B. subtilis mRNA interferase MazF | mRNA | 1NE8 (AA') | 4MDX (A) | PemK_toxin | PF02452 | P96622 | 4 | 111 | 528 | S | D | UB | |
| 4MDX (AB:C) | B. subtilis mRNA interferase MazF | mRNA | 1NE8 (AA') | 4MDX (B) | PemK_toxin | PF02452 | P96622 | 4 | 111 | 1732 | S | D | UB | |
| 4N2Q (A:B) | B. distachyon thylakoid assembly 8 | Zm4 13-mer RNA | 4ME2 (A) | 4N2Q (A) | THA8-like | IPR044190 | I1HB13 | 25 | 236 | 814 | R | D | UB | |
| 4QU6 (A:B) | H. sapiens GRSF1 | synthetic RNA | 2LMI (A) | 4QU6 (A) | RRM_1 | PF00076 | Q12849 | 18 | 82 | 0 | S | D | UB | |
| 4YCP (A:B) | E. coli tRNA-dihydrouridine synthase C | tRNA-Trp | 4BFA (A) | 4YCP (A) | Dus | PF01207 | P33371 | 4 | 308 | 2151 | F | A | UB | |
| 4YVJ (AB:C) | H. influenzae tRNA methyltransferase D | tRNA | 3AXZ (AA') | 4YVJ (A) | tRNA_m1G_MT | PF01746 | P43912 | 22 | 221 | 1130 | R | A | UB | |
| 4YVJ (AB:C) | H. influenzae tRNA methyltransferase D | tRNA | 3AXZ (AA') | 4YVJ (B) | tRNA_m1G_MT | PF01746 | P43912 | 22 | 221 | 1355 | R | A | UB | |
| 4ZT0 (A:B) | S. pyogenes CRISPR-associated endonuclease Cas9 | single-guide RNA | 4CMP (A) | 4ZT0 (A) | Cas9-BH | PF16593 | Q99ZW2 | 62 | 94 | 2105 | F | C | UB | |
| 4ZT0 (A:B) | S. pyogenes CRISPR-associated endonuclease Cas9 | single-guide RNA | 4CMP (A) | 4ZT0 (A) | Cas9_REC | PF16592 | Q99ZW2 | 181 | 712 | 3589 | F | C | UB | |
| 4ZT0 (A:B) | S. pyogenes CRISPR-associated endonuclease Cas9 | single-guide RNA | 4CMP (A) | 4ZT0 (A) | HNH_4 | PF13395 | Q99ZW2 | 821 | 872 | 0 | F | C | UB | |
| 4ZT0 (A:B) | S. pyogenes CRISPR-associated endonuclease Cas9 | single-guide RNA | 4CMP (A) | 4ZT0 (A) | Cas9_RuvC | PF22702 | Q99ZW2 | 925 | 1099 | 262 | F | C | UB | |
| 4ZT0 (A:B) | S. pyogenes CRISPR-associated endonuclease Cas9 | single-guide RNA | 4CMP (A) | 4ZT0 (A) | Cas9_PI | PF16595 | Q99ZW2 | 1102 | 1358 | 2148 | F | C | UB | |
| 5B63 (A:B) | E.coli arginyl-tRNA synthetase | tRNA-Arg | 5YYM:A | 5B63 (A) | Arg_tRNA_synt_N | PF03485 | P11875 | 1 | 87 | 1164 | S | A | UB | |
| 5B63 (A:B) | E.coli arginyl-tRNA synthetase | tRNA-Arg | 5YYM:A | 5B63 (A) | tRNA-synt_1d | PF00750 | P11875 | 95 | 446 | 1674 | S | A | UB | |
| 5B63 (A:B) | E.coli arginyl-tRNA synthetase | tRNA-Arg | 5YYM:A | 5B63 (A) | DALR_1 | PF05746 | P11875 | 460 | 577 | 328 | S | A | UB | |
| 5DET (AB:PQ) | H. sapiens RBPMS | CAC containing ssRNA | 5CYJ (AB) | 5DET (A) | RRM_1 | PF00076 | Q93062 | 26 | 89 | 623 | S | D | UB | |
| 5DET (AB:PQ) | H. sapiens RBPMS | CAC containing ssRNA | 5CYJ (AB) | 5DET (B) | RRM_1 | PF00076 | Q93062 | 26 | 89 | 761 | S | D | UB | |
| 5ED1 (A:BC) | H. sapiens ADAR2 | S. cerevisiae dsRNA | 1ZY7 (A) | 5ED1 (A) | Adenosine-deaminase | PF02137 | P78563 | 72 | 393 | 333 | S | C | UB | |
| 5EIM (A:C) | S. pombe YTH domain of spMmi1 | synthetic RNA | 5H8A (A) | 5EIM (A) | YTH | PF04146 | O74958 | 350 | 477 | 779 | R | D | UB | |
| 5ELS (AC:HI) | H. sapiens KH domain of T-STAR | synthetic RNA | 5EL3 (AB) | 5ELS (A) | Qua1 | PF16274 | O75525 | 50 | 53 | 0 | S | D | UB | |
| 5ELS (AC:HI) | H. sapiens KH domain of T-STAR | synthetic RNA | 5EL3 (AB) | 5ELS (A) | KH_1 | PF00013 | O75525 | 57 | 120 | 1023 | S | D | UB | |
| 5ELS (AC:HI) | H. sapiens KH domain of T-STAR | synthetic RNA | 5EL3 (AB) | 5ELS (C) | Qua1 | PF16274 | O75525 | 50 | 53 | 0 | S | D | UB | |
| 5ELS (AC:HI) | H. sapiens KH domain of T-STAR | synthetic RNA | 5EL3 (AB) | 5ELS (C) | KH_1 | PF00013 | O75525 | 57 | 120 | 1243 | S | D | UB | |
| 5EX7 (A:B) | D. melanogaster Brat NHL domain | hunchback mRNA | 4ZLR (A) | 5EX7 (A) | NHL | PF01436 | Q8MQJ9 | 780 | 807 | 163 | R | D | UB | |
| 5EX7 (A:B) | D. melanogaster Brat NHL domain | hunchback mRNA | 4ZLR (A) | 5EX7 (A) | NHL | PF01436 | Q8MQJ9 | 827 | 856 | 357 | R | D | UB | |
| 5EX7 (A:B) | D. melanogaster Brat NHL domain | hunchback mRNA | 4ZLR (A) | 5EX7 (A) | NHL | PF01436 | Q8MQJ9 | 871 | 898 | 349 | R | D | UB | |
| 5EX7 (A:B) | D. melanogaster Brat NHL domain | hunchback mRNA | 4ZLR (A) | 5EX7 (A) | NHL | PF01436 | Q8MQJ9 | 914 | 941 | 407 | R | D | UB | |
| 5EX7 (A:B) | D. melanogaster Brat NHL domain | hunchback mRNA | 4ZLR (A) | 5EX7 (A) | NHL | PF01436 | Q8MQJ9 | 957 | 985 | 449 | R | D | UB | |
| 5F5H (A:C) | M. musculus Roquin-1 | Ox40 3'-UTR | 4QI0 (A) | 5F5H (A) | Roquin_1_2-like_ROQ | PF21206 | Q4VGL6 | 182 | 268 | 1614 | R | C | UB | |
| 5F5H (A:C) | M. musculus Roquin-1 | Ox40 3'-UTR | 4QI0 (A) | 5F5H (A) | ROQ_II | PF18386 | Q4VGL6 | 271 | 325 | 0 | R | C | UB | |
| 5GXH (A:B) | H. sapiens Gemin5 | Pre-snRNAs | 5TEE:A | 5GXH (A) | WD40 | PF00400 | Q8TEQ6 | 54 | 95 | 80 | R | D | UB | |
| 5GXH (A:B) | H. sapiens Gemin5 | Pre-snRNAs | 5TEE:A | 5GXH (A) | MIOS_WD40 | PF21720 | Q8TEQ6 | 85 | 209 | 45 | R | D | UB | |
| 5GXH (A:B) | H. sapiens Gemin5 | Pre-snRNAs | 5TEE:A | 5GXH (A) | WD40 | PF00400 | Q8TEQ6 | 239 | 255 | 13 | R | D | UB | |
| 5GXH (A:B) | H. sapiens Gemin5 | Pre-snRNAs | 5TEE:A | 5GXH (A) | ANAPC4_WD40 | PF12894 | Q8TEQ6 | 388 | 480 | 394 | R | D | UB | |
| 5GXH (A:B) | H. sapiens Gemin5 | Pre-snRNAs | 5TEE:A | 5GXH (A) | ANAPC4_WD40 | PF12894 | Q8TEQ6 | 526 | 589 | 233 | R | D | UB | |
| 5GXH (A:B) | H. sapiens Gemin5 | Pre-snRNAs | 5TEE:A | 5GXH (A) | WD40 | PF00400 | Q8TEQ6 | 629 | 668 | 204 | R | D | UB | |
| 5GXH (A:B) | H. sapiens Gemin5 | Pre-snRNAs | 5TEE:A | 5GXH (A) | WD40 | PF00400 | Q8TEQ6 | 672 | 710 | 285 | R | D | UB | |
| 5HO4 (A:B) | H. sapiens hnRNP A2/B1 | substrate RNA | 1X4B:A | 5HO4 (A) | RRM_1 | PF00076 | P22626 | 23 | 92 | 907 | S | D | UB | |
| 5HO4 (A:B) | H. sapiens hnRNP A2/B1 | substrate RNA | 1X4B:A | 5HO4 (A) | RRM_1 | PF00076 | P22626 | 114 | 183 | 0 | S | D | UB | |
| 5HR7 (A:D) | E. coli RNA methyltransferase RlmN | tRNA-Glu | 3RFA (A) | 5HR7 (A) | RlmN_N | PF21016 | P36979 | 18 | 77 | 649 | R | A | UB | |
| 5HR7 (A:D) | E. coli RNA methyltransferase RlmN | tRNA-Glu | 3RFA (A) | 5HR7 (A) | Radical_SAM | PF04055 | P36979 | 119 | 298 | 1961 | R | A | UB | |
| 5LTA (A:E) | T. thermophila DEAH-box heicase Prp43 | Synthetic RNA | 5LTJ (A) | 5LTA (A) | DEAD | PF00270 | G0RY84 | 99 | 260 | 722 | F | D | UB | |
| 5LTA (A:E) | T. thermophila DEAH-box heicase Prp43 | Synthetic RNA | 5LTJ (A) | 5LTA (A) | Helicase_C | PF00271 | G0RY84 | 291 | 437 | 874 | F | D | UB | |
| 5LTA (A:E) | T. thermophila DEAH-box heicase Prp43 | Synthetic RNA | 5LTJ (A) | 5LTA (A) | HA2_N | PF04408 | G0RY84 | 499 | 527 | 137 | F | D | UB | |
| 5LTA (A:E) | T. thermophila DEAH-box heicase Prp43 | Synthetic RNA | 5LTJ (A) | 5LTA (A) | HA2_C | PF21010 | G0RY84 | 528 | 587 | 309 | F | D | UB | |
| 5LTA (A:E) | T. thermophila DEAH-box heicase Prp43 | Synthetic RNA | 5LTJ (A) | 5LTA (A) | OB_NTP_bind | PF07717 | G0RY84 | 653 | 731 | 398 | F | D | UB | |
| 5SZE (A:C) | Aquifex aeolicus Hfq-RNA | PolyU | 5SVD (A) | 5SZE (A) | Hfq | PF17209 | O66512 | 5 | 68 | 502 | R | D | UB | |
| 5T16 (ABCDEF:GH) | S. cerevisiae RNase III | RNA substrate analog | 1T4O (A) | 5T16 (A) | Ribonuclease_3 | PF00636 | Q02555 | 238 | 331 | 1064 | R | C | UB | |
| 5T16 (ABCDEF:GH) | S. cerevisiae RNase III | RNA substrate analog | 1T4O (A) | 5T16 (A) | dsrm | PF00035 | Q02555 | 370 | 435 | 1604 | R | C | UB | |
| 5T16 (ABCDEF:GH) | S. cerevisiae RNase III | RNA substrate analog | 1T4O (A) | 5T16 (B) | Ribonuclease_3 | PF00636 | Q02555 | 238 | 331 | 1010 | R | C | UB | |
| 5T16 (ABCDEF:GH) | S. cerevisiae RNase III | RNA substrate analog | 1T4O (A) | 5T16 (B) | dsrm | PF00035 | Q02555 | 370 | 435 | 1590 | R | C | UB | |
| 5T16 (ABCDEF:GH) | S. cerevisiae RNase III | RNA substrate analog | 1T4O (A) | 5T16 (C) | RNase_3_N | PF18497 | Q02555 | 44 | 153 | 284 | R | C | UB | |
| 5T16 (ABCDEF:GH) | S. cerevisiae RNase III | RNA substrate analog | 1T4O (A) | 5T16 (D) | RNase_3_N | PF18497 | Q02555 | 44 | 153 | 134 | R | C | UB | |
| 5T16 (ABCDEF:GH) | S. cerevisiae RNase III | RNA substrate analog | 1T4O (A) | 5T16 (E) | RNase_3_N | PF18497 | Q02555 | 44 | 153 | 276 | R | C | UB | |
| 5T16 (ABCDEF:GH) | S. cerevisiae RNase III | RNA substrate analog | 1T4O (A) | 5T16 (F) | RNase_3_N | PF18497 | Q02555 | 44 | 153 | 125 | R | C | UB | |
| 5T8Y (B:X) | B. subtilis Epoxyqueuosine reductase | anticodon stem loop of tRN | 5D08 (A) | 5T8Y (B) | QueG_DUF1730 | PF08331 | P97030 | 57 | 132 | 0 | R | A | UB | |
| 5T8Y (B:X) | B. subtilis Epoxyqueuosine reductase | anticodon stem loop of tRN | 5D08 (A) | 5T8Y (B) | HEAT_PBS | PF03130 | P97030 | 332 | 358 | 0 | R | A | UB | |
| 5V7C (B:C) | H. sapiens LARP1-unique domain DM15 | 5'TOP motif | 5V87 (A) | 5V7C (B) | LARP1_HEAT | PF21071 | Q6PKG0 | 874 | 1018 | 436 | R | D | UB | |
| 5W0M (A:H) | H. sapiens TUT7 catalytic module | PolyU | 5W0B (A) | 5W0M (A) | MTPAP-like_central | PF22600 | Q5VYS8 | 1001 | 1139 | 905 | R | D | UB | |
| 5W0M (A:H) | H. sapiens TUT7 catalytic module | PolyU | 5W0B (A) | 5W0M (A) | PAP_assoc | PF03828 | Q5VYS8 | 1233 | 1286 | 129 | R | D | UB | |
| 5W0M (A:H) | H. sapiens TUT7 catalytic module | PolyU | 5W0B (A) | 5W0M (A) | zf-CCHC | PF00098 | Q5VYS8 | 1345 | 1362 | 375 | R | D | UB | |
| 5WT1 (A:C) | P. abysi Trm5a | tRNA-Phe | 5HJM (A) | 5WT1 (A) | Trm5_N | PF18093 | Q9V2G1 | 3 | 45 | 887 | S | A | UB | |
| 5WTK (A:B) | L. shahii CRISPR-associated endoribonuclease C2c2 | CRISPR RNA | 5WTJ (A) | 5WTK (A) | Cas13a_endoribonucle | IPR053395 | P0DOC6 | 5 | 1377 | 3572 | F | C | UB | |
| 5WTY (A:C) | S. cerevisiae nucleolar protein 9 | 18s rRNA | 5SVD (A) | 5WTY (A) | PUF_NOP9 | PF22493 | P47077 | 95 | 604 | 3205 | F | B | UB | |
| 5WWX (A:C) | H. sapiens KH2 domain of MEX-3C | 5-mer RNA | 5WWZ (A) | 5WWX (A) | KH_1 | PF00013 | Q5U5Q3 | 328 | 389 | 1183 | R | D | UB | |
| 5X6B (EFIJ:P) | M. jannaschii SepCysE-SepCysS | tRNA-Cys | 3WKR (ABCD) | 2ZZN* (D) | 5X6B (E) | DUF2100 | PF09873 | Q58876 | 34 | 101 | 0 | R | A | UU |
| 5X6B (EFIJ:P) | M. jannaschii SepCysE-SepCysS | tRNA-Cys | 3WKR (ABCD) | 2ZZN* (D) | 5X6B (F) | DUF2100 | PF09873 | Q58876 | 34 | 210 | 1960 | R | A | UU |
| 5X6B (EFIJ:P) | M. jannaschii SepCysE-SepCysS | tRNA-Cys | 3WKR (ABCD) | 2ZZN* (D) | 5X6B (I) | SepSecS | PF05889 | Q59072 | 87 | 374 | 1630 | R | A | UU |
| 5X6B (IJE:P) | M. jannaschii SepCysE-SepCysS | tRNA-Cys | 3WKR (ABCD) | 2ZZN* (D) | 5X6B (J) | SepSecS | PF05889 | Q59072 | 87 | 374 | 187 | R | A | UU |
| 5ZQ8 (A:D) | S. pneumoniae RlmCD | U747 stem-loop RNA | 5XJ1 (A) | 5ZQ8 (A) | TRAM | PF01938 | Q97R12 | 2 | 57 | 0 | R | C | UB | |
| 5ZQ8 (A:D) | S. pneumoniae RlmCD | U747 stem-loop RNA | 5XJ1 (A) | 5ZQ8 (A) | tRNA_U5-meth_tr | PF05958 | Q97R12 | 87 | 451 | 1953 | R | C | UB | |
| 5ZSC (A:C) | M. mulatta Toll-like receptor 7 | CCUUCC RNA | 6IF5 (A) | 5ZSC (A) | LRR_8 | PF13855 | B3Y653 | 273 | 326 | 0 | R | D | UB | |
| 5ZSC (A:C) | M. mulatta Toll-like receptor 7 | CCUUCC RNA | 6IF5 (A) | 5ZSC (A) | LRR_8 | PF13855 | B3Y653 | 496 | 554 | 0 | R | D | UB | |
| 5ZSC (A:C) | M. mulatta Toll-like receptor 7 | CCUUCC RNA | 6IF5 (A) | 5ZSC (A) | LRR_8 | PF13855 | B3Y653 | 675 | 735 | 0 | R | D | UB | |
| 5ZSC (A:C) | M. mulatta Toll-like receptor 7 | CCUUCC RNA | 6IF5 (A) | 5ZSC (A) | LRR_8 | PF13855 | B3Y653 | 723 | 785 | 0 | R | D | UB | |
| 5ZSC (A:C) | M. mulatta Toll-like receptor 7 | CCUUCC RNA | 6IF5 (A) | 5ZSC (B) | LRR_8 | PF13855 | B3Y653 | 273 | 326 | 0 | R | D | UB | |
| 5ZSC (A:C) | M. mulatta Toll-like receptor 7 | CCUUCC RNA | 6IF5 (A) | 5ZSC (B) | LRR_8 | PF13855 | B3Y653 | 496 | 554 | 0 | R | D | UB | |
| 5ZSC (A:C) | M. mulatta Toll-like receptor 7 | CCUUCC RNA | 6IF5 (A) | 5ZSC (B) | LRR_8 | PF13855 | B3Y653 | 675 | 735 | 0 | R | D | UB | |
| 5ZSC (A:C) | M. mulatta Toll-like receptor 7 | CCUUCC RNA | 6IF5 (A) | 5ZSC (B) | LRR_8 | PF13855 | B3Y653 | 723 | 785 | 0 | R | D | UB | |
| 5ZW4 (A:D) | B. subtilis TrmR | tRNA fragment | 5ZW3 (A) | 5ZW4 (A) | Methyltransf_3 | PF01596 | O32036 | 17 | 216 | 762 | R | A | UB | |
| 6A4E (A:B) | C. psychrerythraea Oligoribonuclease | U-rich RNA | 6A4D (A) | 6A4E (A) | RNase_T | PF00929 | Q47VZ4 | 9 | 171 | 759 | R | D | UB | |
| 6A6J (A:B) | D. rerio cold shock domain of Ybx1 | 6mer m5C RNA | 1H95 (A) | 6A6J (A) | CSD | PF00313 | P67809 | 59 | 128 | 686 | R | D | UB | |
| 6AAX (A:B) | H. Sapiens Mitochondrial transcription factor B1 | 12s rRNA | 6AAS (A) | 6AAX (A) | RrnaAD | PF00398 | Q8WVM0 | 35 | 303 | 1758 | B | BU | ||
| 6D12 (B:C) | H. sapiens xRRM domain of human Larp7 | 7SK stem-loop 4 RNA | 5KNW (A) | 6D12 (B) | RRM_3 | PF08777 | Q4G0J3 | 454 | 548 | 1404 | S | C | UB | |
| 6DCB (A:B) | H. sapiens methylphosphate capping enzyme | 5' end of 7SK RNA | 5UNA (A) | 6DCB (A) | Methyltransf_31 | PF13847 | Q7L2J0 | 443 | 492 | 0 | R | C | UB | |
| 6DCB (A:B) | H. sapiens methylphosphate capping enzyme | 5' end of 7SK RNA | 5UNA (A) | 6DCB (A) | Bin3 | PF06859 | Q7L2J0 | 575 | 683 | 501 | R | C | UB | |
| 6FQ3 (A:B) | D. rerio E3 ubiquitin-protein ligase TRIM71 | lin-29A 5'UTR | 6FPT (A) | 6FQ3 (A) | Filamin | PF00630 | E7FAM5 | 437 | 533 | 0 | S | C | UB | |
| 6FQ3 (A:B) | D. rerio E3 ubiquitin-protein ligase TRIM71 | lin-29A 5'UTR | 6FPT (A) | 6FQ3 (A) | NHL | PF01436 | E7FAM5 | 562 | 589 | 329 | S | C | UB | |
| 6FQ3 (A:B) | D. rerio E3 ubiquitin-protein ligase TRIM71 | lin-29A 5'UTR | 6FPT (A) | 6FQ3 (A) | NHL | PF01436 | E7FAM5 | 609 | 636 | 283 | S | C | UB | |
| 6FQ3 (A:B) | D. rerio E3 ubiquitin-protein ligase TRIM71 | lin-29A 5'UTR | 6FPT (A) | 6FQ3 (A) | NHL | PF01436 | E7FAM5 | 656 | 683 | 269 | S | C | UB | |
| 6FQ3 (A:B) | D. rerio E3 ubiquitin-protein ligase TRIM71 | lin-29A 5'UTR | 6FPT (A) | 6FQ3 (A) | NHL | PF01436 | E7FAM5 | 703 | 730 | 160 | S | C | UB | |
| 6FQ3 (A:B) | D. rerio E3 ubiquitin-protein ligase TRIM71 | lin-29A 5'UTR | 6FPT (A) | 6FQ3 (A) | NHL | PF01436 | E7FAM5 | 750 | 777 | 253 | S | C | UB | |
| 6FQ3 (A:B) | D. rerio E3 ubiquitin-protein ligase TRIM71 | lin-29A 5'UTR | 6FPT (A) | 6FQ3 (A) | NHL | PF01436 | E7FAM5 | 797 | 824 | 10 | S | C | UB | |
| 6GC5 (A:E) | H. sapiens HuR RRM3 | AU-rich RNA | 6GD1 (A) | 6GC5 (A) | RRM_1 | PF00076 | Q15717 | 246 | 316 | 1099 | R | D | UB | |
| 6HAU (AB:D) | H. saimiri mRNA export factor ICP27 homolog | MRE fragment of PAN R | 6HAT (AB) | 6HAU (A) | Herpes_UL69 | PF05459 | P13199 | 197 | 415 | 548 | R | D | UB | |
| 6HAU (AB:D) | H. saimiri mRNA export factor ICP27 homolog | MRE fragment of PAN R | 6HAT (AB) | 6HAU (B) | Herpes_UL69 | PF05459 | P13199 | 197 | 415 | 586 | R | D | UB | |
| 6HTU (ABC:DF) | H. sapiens hStau1 dsRBD3-4 | ARF1 RNA | 6HU6:AE | 6HTU (A) | dsrm | PF00035 | O95793 | 185 | 249 | 1397 | C | BU | ||
| 6HTU (ABC:DF) | H. sapiens hStau1 dsRBD3-4 | ARF1 RNA | 6HU6:AE | 6HTU (B) | dsrm | PF00035 | O95793 | 185 | 249 | 960 | C | BU | ||
| 6HTU (ABC:DF) | H. sapiens hStau1 dsRBD3-4 | ARF1 RNA | 6HU6:AE | 6HTU (C) | dsrm | PF00035 | O95793 | 287 | 352 | 873 | C | BU | ||
| 6I0V (A:B) | D. melanogaster DmTailor (384) | 8-mer RNA | 6I0S (A) | 6I0V (A) | MTPAP-like_central | PF22600 | Q9VI58 | 216 | 362 | 1003 | R | D | UB | |
| 6L1W (A:C) | M. musculus Zinc finger CCCH-type antiviral protein 1 | CG rich RNA | 3U9G (A) | 6L1W (A) | HTH_53 | PF18606 | Q3UPF5 | 5 | 66 | 0 | S | D | UB | |
| 6L1W (A:C) | M. musculus Zinc finger CCCH-type antiviral protein 1 | CG rich RNA | 3U9G (A) | 6L1W (A) | zf-CCCH_8 | PF18633 | Q3UPF5 | 143 | 170 | 453 | S | D | UB | |
| 6L5N (A:C) | H. sapiens nucleolar RNA helicase 2 | polyU | 6L5M (A) | 6L5N (A) | DEAD | PF00270 | Q9NR30 | 210 | 385 | 793 | R | D | UB | |
| 6L5N (A:C) | H. sapiens nucleolar RNA helicase 2 | polyU | 6L5M (A) | 6L5N (A) | Helicase_C | PF00271 | Q9NR30 | 423 | 532 | 499 | R | D | UB | |
| 6LLB (A:C) | M. psychrophilus MPY-RNase J | 6-mer RNA | 5HAA (A) | 6LLB (A) | Lactamase_B_2 | PF12706 | NA | 96 | 199 | 196 | R | D | UB | |
| 6LLB (A:C) | M. psychrophilus MPY-RNase J | 6-mer RNA | 5HAA (A) | 6LLB (A) | RMMBL | PF07521 | NA | 399 | 448 | 85 | R | D | UB | |
| 6LT7 (AB:C) | H. sapiens ribonuclease P protein subunit p20 | P3 domain of lncRNA RM | 6CWX (AB) | 6LT7 (A) | Rpp20 | PF12328 | O75817 | 32 | 133 | 3110 | S | D | UB | |
| 6LT7 (AB:C) | H. sapiens ribonuclease P protein subunit p20 | P3 domain of lncRNA RM | 6CWX (AB) | 6LT7 (B) | Alba | PF01918 | Q9BUL9 | 36 | 101 | 1975 | S | D | UB | |
| 6LVR (A:C) | A. thaliana RNase P1 | tRNA-Phe | 4G24 (A) | 1I9V (A) | 6LVR (A) | PPR_long | PF17177 | Q66GI4 | 94 | 293 | 1055 | F | A | UU |
| 6PZQ (AB:IJ) | H. Respiratory syncytial Virus M-21 Protein | Short Positive-Sense Gene- | 6G0Y (AE) | 6PZQ (A) | Pneumovirus_M2 | PF06436 | P04545 | 29 | 174 | 0 | R | C | UB | |
| 6PZQ (AB:IJ) | H. Respiratory syncytial Virus M-21 Protein | Short Positive-Sense Gene- | 6G0Y (AE) | 6PZQ (B) | Pneumovirus_M2 | PF06436 | P04545 | 29 | 174 | 77 | R | C | UB | |
| 6R9P (A:B) | S. cerevisae apo Pan2 pseudoubiquitin hydrolase | AAUUAA RNA | 6R9I (A) | 6R9P (A) | UCH_1 | PF13423 | P53010 | 505 | 829 | 0 | R | D | UB | |
| 6R9P (A:B) | S. cerevisae apo Pan2 pseudoubiquitin hydrolase | AAUUAA RNA | 6R9I (A) | 6R9P (A) | RNase_T | PF00929 | P53010 | 907 | 1079 | 974 | R | D | UB | |
| 6RTI (A:X) | H. sapiens GCPII | A9gRNA aptamer (43-ME | 2C6C:A | 6RTI (A) | PA | PF02225 | Q04609 | 170 | 261 | 446 | R | C | UB | |
| 6RTI (A:X) | H. sapiens GCPII | A9gRNA aptamer (43-ME | 2C6C:A | 6RTI (A) | Peptidase_M28 | PF04389 | Q04609 | 357 | 564 | 570 | R | C | UB | |
| 6RTI (A:X) | H. sapiens GCPII | A9gRNA aptamer (43-ME | 2C6C:A | 6RTI (A) | TFR_dimer | PF04253 | Q04609 | 627 | 747 | 529 | R | C | UB | |
| 6SY4 (AB:C) | E. coli TetR | TetR-binding aptamer K1 | 3ZQI (AB) | 6SY4 (A) | TetR_N | PF00440 | P04483 | 9 | 55 | 837 | S | C | UB | |
| 6SY4 (AB:C) | E. coli TetR | TetR-binding aptamer K1 | 3ZQI (AB) | 6SY4 (A) | TetR_C_1 | PF02909 | P04483 | 68 | 201 | 0 | S | C | UB | |
| 6SY4 (AB:C) | E. coli TetR | TetR-binding aptamer K1 | 3ZQI (AB) | 6SY4 (B) | TetR_N | PF00440 | P04483 | 9 | 55 | 865 | S | C | UB | |
| 6SY4 (AB:C) | E. coli TetR | TetR-binding aptamer K1 | 3ZQI (AB) | 6SY4 (B) | TetR_C_1 | PF02909 | P04483 | 68 | 201 | 0 | S | C | UB | |
| 6U6Y (AD:EH) | H. sapiens SAMHD1 | ribo(CGCCU)-oligonucleoti | 5AO3:AB | 6U6Y (A) | HD | PF01966 | Q9Y3Z3 | 164 | 274 | 72 | R | D | UB | |
| 6U6Y (AD:EH) | H. sapiens SAMHD1 | ribo(CGCCU)-oligonucleoti | 5AO3:AB | 6U6Y (D) | HD | PF01966 | Q9Y3Z3 | 164 | 274 | 78 | R | D | UB | |
| 6U9X (D:H) | T. brucei MERS1 | G rich RNA | 6NL1 (A) | 6U9X (D) | NUDIX | PF00293 | B6SBM0 | 209 | 338 | 1482 | S | D | UB | |
| 6WXY (BC:A) | T. succinifaciens card1 nuclease | crRNA | 6WXW (A) | 6WXY (B) | Card1_endonuc | PF09002 | F2NWD3 | 246 | 372 | 52 | R | D | UB | |
| 6WXY (BC:A) | T. succinifaciens card1 nuclease | crRNA | 6WXW (A) | 6WXY (C) | Card1_endonuc | PF09002 | F2NWD3 | 246 | 372 | 54 | R | D | UB | |
| 6ZDP (A:B) | C. tropicalis telomerase reverse transcriptase | TWJ fragment of telomeric | 6ZD6 (A) | 6ZDP (A) | Telomerase_RBD | PF12009 | C5MCQ7 | 257 | 388 | 1532 | F | C | UB | |
| 6ZDP (A:B) | C. tropicalis telomerase reverse transcriptase | TWJ fragment of telomeric | 6ZD6 (A) | 6ZDP (A) | RVT_1 | PF00078 | C5MCQ7 | 598 | 734 | 0 | F | C | UB | |
| 6ZOT (AB:C) | H. sapiens YTH domain-containing family protein 3 | m6A RNA | 8BS5:A | 6ZOT (A) | YTH | PF04146 | Q7Z739 | 416 | 551 | 196 | R | D | UB | |
| 6ZOT (AB:C) | H. sapiens YTH domain-containing family protein 3 | m6A RNA | 8BS5:A | 6ZOT (B) | YTH | PF04146 | Q7Z739 | 416 | 551 | 1193 | R | D | UB | |
| 7C45 (A:D) | T. brucei RNase D ribonuclease | Guide RNA U12 | 7C42 (A) | 7C45 (A) | DNA_pol_A_exo1 | PF01612 | Q38DE2 | 55 | 244 | 1355 | F | D | UB | |
| 7C45 (A:D) | T. brucei RNase D ribonuclease | Guide RNA U12 | 7C42 (A) | 7C45 (A) | zf-CCHC | PF00098 | Q38DE2 | 318 | 335 | 625 | F | D | UB | |
| 7DOL (A:C) | M. genitalium Ribonuclease R | dsRNA | 7DCY (A) | 7DOL (A) | RNB | PF00773 | P47350 | 264 | 593 | 2034 | R | D | UB | |
| 7DOL (A:C) | M. genitalium Ribonuclease R | dsRNA | 7DCY (A) | 7DOL (A) | S1 | PF00575 | P47350 | 640 | 725 | 10 | R | D | UB | |
| 7E8O (AB:X) | P. bacterium RNA-free ribonuclease P | histidine pre-tRNA | 7E8K (AB) | 7E8O (A) | PIN_5 | PF08745 | A0A1G2XP69 | 16 | 202 | 546 | R | A | UB | |
| 7E8O (AB:X) | P. bacterium RNA-free ribonuclease P | histidine pre-tRNA | 7E8K (AB) | 7E8O (B) | PIN_5 | PF08745 | A0A1G2XP69 | 16 | 202 | 325 | R | A | UB | |
| 7EIU (A:C) | S. pombe Meiosis protein mei2 RRM3 | meiRNA | 7EIO (A) | 7EIU (A) | RRM_2 | PF04059 | P08965 | 596 | 692 | 876 | R | D | UB | |
| 7K5L(A:R) | Ebola virus Matrix protein VP40 | HSP RNA oligonucleotide | 4LDB:A | 7K5L(A) | VP40 | PF07447 | Q05128 | 69 | 192 | 474 | S | D | UB | |
| 7K98 (ABDE:CF) | M. tuberculosis PheRS | tRNA-Phe | 7DAW (ABCD) | 7K98 (A) | Phe_tRNA-synt_N | PF02912 | P9WFU3 | 22 | 90 | 1047 | F | A | UB | |
| 7K98 (ABDE:CF) | M. tuberculosis PheRS | tRNA-Phe | 7DAW (ABCD) | 7K98 (A) | tRNA-synt_2d | PF01409 | P9WFU3 | 94 | 337 | 1044 | F | A | UB | |
| 7K98 (ABDE:CF) | M. tuberculosis PheRS | tRNA-Phe | 7DAW (ABCD) | 7K98 (B) | tRNA_bind | PF01588 | P9WFU1 | 50 | 153 | 0 | F | A | UB | |
| 7K98 (ABDE:CF) | M. tuberculosis PheRS | tRNA-Phe | 7DAW (ABCD) | 7K98 (B) | B3_4 | PF03483 | P9WFU1 | 222 | 395 | 265 | F | A | UB | |
| 7K98 (ABDE:CF) | M. tuberculosis PheRS | tRNA-Phe | 7DAW (ABCD) | 7K98 (B) | B5 | PF03484 | P9WFU1 | 419 | 484 | 0 | F | A | UB | |
| 7K98 (ABDE:CF) | M. tuberculosis PheRS | tRNA-Phe | 7DAW (ABCD) | 7K98 (B) | tRNA_synthFbeta | PF17759 | P9WFU1 | 487 | 722 | 487 | F | A | UB | |
| 7K98 (ABDE:CF) | M. tuberculosis PheRS | tRNA-Phe | 7DAW (ABCD) | 7K98 (D) | Phe_tRNA-synt_N | PF02912 | P9WFU3 | 22 | 90 | 1054 | F | A | UB | |
| 7K98 (ABDE:CF) | M. tuberculosis PheRS | tRNA-Phe | 7DAW (ABCD) | 7K98 (D) | tRNA-synt_2d | PF01409 | P9WFU3 | 94 | 337 | 1076 | F | A | UB | |
| 7K98 (ABDE:CF) | M. tuberculosis PheRS | tRNA-Phe | 7DAW (ABCD) | 7K98 (E) | tRNA_bind | PF01588 | P9WFU1 | 50 | 153 | 0 | F | A | UB | |
| 7K98 (ABDE:CF) | M. tuberculosis PheRS | tRNA-Phe | 7DAW (ABCD) | 7K98 (E) | B3_4 | PF03483 | P9WFU1 | 222 | 395 | 253 | F | A | UB | |
| 7K98 (ABDE:CF) | M. tuberculosis PheRS | tRNA-Phe | 7DAW (ABCD) | 7K98 (E) | tRNA_synthFbeta | PF17759 | P9WFU1 | 487 | 722 | 487 | F | A | UB | |
| 7K98 (ABDE:CF) | M. tuberculosis PheRS | tRNA-Phe | 7DAW (ABCD) | 7K98 (E) | FDX-ACB | PF03147 | P9WFU1 | 737 | 830 | 1659 | F | A | UB | |
| 7KFN (AD:BC) | H. sapiens adenosine deaminase | dsRNA Gli1 8AZ+1W5 | 1ZY7 (A) | 7KFN (A) | A_deamin | PF02137 | P78563 | 370 | 731 | 2648 | S | C | UB | |
| 7KFN (AD:BC) | H. sapiens adenosine deaminase | dsRNA Gli1 8AZ+1W5 | 1ZY7 (A) | 7KFN (D) | A_deamin | PF02137 | P78563 | 370 | 731 | 71 | S | C | UB | |
| 7KKV (A:B) | A. halodurans OapB protein | OLE RNA target | 7K9B (A) | 7KKV (A) | Ribosomal_eL14_KO | IPR041985 | Q9KGD7 | 5 | 80 | 1365 | R | C | UB | |
| 7KL3 (A:B) | Influenza A virus california PA endonuclease | RNA oligomer AG*CAUC | 5CZN (A) | 7KL3 (A) | Flu_PA | PF00603 | A0A5J6VBC3 | 21 | 183 | 826 | R | D | UB | |
| 7L6T (A:C) | SARS-CoV-2 Nsp16/10 Heterodimer | mRNA | 7C2I (A) | 7L6T (A) | CoV_Methyltr_2 | PF06460 | P0DTD1 | 6800 | 7096 | 1120 | R | D | UB | |
| 7MJW (A:M) | B. uniformis tRNA-2-methylthio-N(6)-dimethylallyladen | tRNA | 7MJZ (A) | 7MJW (A) | UPF0004 | PF00919 | A0A174NUT3 | 19 | 117 | 772 | S | A | UB | |
| 7MJW (A:M) | B. uniformis tRNA-2-methylthio-N(6)-dimethylallyladen | tRNA | 7MJZ (A) | 7MJW (A) | Radical_SAM | PF04055 | A0A174NUT3 | 165 | 339 | 327 | S | A | UB | |
| 7MJW (A:M) | B. uniformis tRNA-2-methylthio-N(6)-dimethylallyladen | tRNA | 7MJZ (A) | 7MJW (A) | TRAM | PF01938 | A0A174NUT3 | 393 | 455 | 1037 | S | A | UB | |
| 7OG0 (A:EE') | H. influenzae SapA | dsRNA | 8TV8 (A) | 7OG0 (A) | SBP_bac_S | PF00496 | Q4QL73 | 46 | 446 | 421 | S | C | UB | |
| 7OM6 (A:CD) | T. asigna virus RdRP domain | RNA oligonucleotide | 7OM2 (A) | 7OM6 (A) | Permu_RdRp_palm | PF22152 | Q6A562 | 160 | 516 | 588 | R | C | UB | |
| 7OM6 (A:CD) | T. asigna virus RdRP domain | RNA oligonucleotide | 7OM2 (A) | 7OM6 (A) | Permu_RdRp_thumb | PF22260 | Q6A562 | 536 | 638 | 922 | R | C | UB | |
| 7P0V (A:B) | H. sapiens SF3A1 ubiquitin-like domain | U1 snRNA SL-4 | 7P08 (A) | 8ID2* (C) | 7P0V (A) | ubiquitin | PF00240 | Q15459 | 717 | 788 | 1004 | S | C | UU |
| 7V4G (A:D) | H. sapiens RNA demethylase ALKBH5 | m6A-containing ssRNA | 4O61 (A) | 7V4G (A) | 2OG-FeII_Oxy_2 | PF13532 | Q6P6C2 | 88 | 292 | 1529 | R | D | UB | |
| 7VKI (A:B) | H. Sapiens ESRP1 | 12-mer RNA | 2DHA (A) | 7VKI (A) | RRM1 | PRU00176 | Q6NXG1 | 326 | 406 | 632 | R | D | UB | |
| 7VKL (A:B) | M. Musculus MmIMP3-RRM12 | zipcode RNA | 6GQE (A) | 7VKL (A) | KH_1 | PF00013 | Q9CPN8 | 197 | 262 | 1191 | R | D | UB | |
| 7VKL (A:B) | M. Musculus MmIMP3-RRM12 | zipcode RNA | 6GQE (A) | 7VKL (A) | KH_1 | PF00013 | Q9CPN8 | 278 | 345 | 0 | R | D | UB | |
| 7VSJ (A:B) | M. Musculus MmIMP3-RRM12 | 9-mer RNA | 6FQ1 (A) | 7VSJ (A) | RRM_1 | PF00076 | Q9CPN8 | 83 | 150 | 0 | R | D | UB | |
| 7XD8 (A:BC) | Dengue Virus 2 NS5 | 30-mer RNA | 6KR2 (A) | 7XD8 (A) | Flavi_NS5 | PF00972 | Q91H74 | 268 | 700 | 2315 | F | C | UB | |
| 7XD8 (A:BC) | Dengue Virus 2 NS5 | 30-mer RNA | 6KR2 (A) | 7XD8 (A) | Flavi_NS5_thumb | PF20483 | Q91H74 | 704 | 867 | 1391 | F | C | UB | |
| 7XWZ (A:CD) | SARS-CoV-2 N-NTD Nucleoprotein | dsRNA | 7XX1 (A) | 7XWZ (A) | CoV_nucleocap | PF00937 | P0DTC9 | 48 | 171 | 811 | S | C | UB | |
| 7Y7Q (AB:CED) | N. Crasa RNA-dependent RNA polymerase | siRNAs | 2J7N (A) | 7Y7Q (A) | RdRP | PF05183 | Q9Y7G6 | 510 | 1170 | 0 | R | D | UB | |
| 7Y7Q (AB:CED) | N. Crasa RNA-dependent RNA polymerase | siRNAs | 2J7N (A) | 7Y7Q (B) | RdRP | PF05183 | Q9Y7G6 | 510 | 1170 | 1003 | R | D | UB | |
| 7YSE (ABCD:EF) | E. coli glycyl-tRNA synthetase | tRNA-Gly | 7EIV (ABCD) | 7F36* (F) | 7YSE (A) | tRNA-synt_2e | PF02091 | P00960 | 9 | 292 | 1611 | F | A | UU |
| 7YSE (ABCD:EF) | E. coli glycyl-tRNA synthetase | tRNA-Gly | 7EIV (ABCD) | 7F36* (F) | 7YSE (B) | tRNA-synt_2e | PF02091 | P00960 | 9 | 292 | 1616 | F | A | UU |
| 7YSE (ABCD:EF) | E. coli glycyl-tRNA synthetase | tRNA-Gly | 7EIV (ABCD) | 7F36* (F) | 7YSE (C) | tRNA_synt_2f | PF02092 | P00961 | 6 | 551 | 2199 | F | A | UU |
| 7YSE (ABCD:EF) | E. coli glycyl-tRNA synthetase | tRNA-Gly | 7EIV (ABCD) | 7F36* (F) | 7YSE (C) | DALR_1 | PF05746 | P00961 | 579 | 685 | 994 | F | A | UU |
| 7YSE (ABCD:EF) | E. coli glycyl-tRNA synthetase | tRNA-Gly | 7EIV (ABCD) | 7F36* (F) | 7YSE (D) | tRNA_synt_2f | PF02092 | P00961 | 6 | 551 | 2053 | F | A | UU |
| 7YSE (ABCD:EF) | E. coli glycyl-tRNA synthetase | tRNA-Gly | 7EIV (ABCD) | 7F36* (F) | 7YSE (D) | DALR_1 | PF05746 | P00961 | 579 | 685 | 626 | F | A | UU |
| 7ZLQ (A:DE) | H. Sapiens ADAR1-dsRBD3 | dsRNA | 2MDR:A | 7ZLQ (A) | dsrm | PF00035 | P55265 | 727 | 792 | 557 | R | C | UB | |
| 8AF0 (AB:CD) | H. Sapiens Angiogenin | dsRNA | 5M9T (A) | 8AF0 (A) | RnaseA | PF00074 | P03950 | 28 | 140 | 200 | R | C | UB | |
| 8AF0 (AB:CD) | H. Sapiens Angiogenin | dsRNA | 5M9T (A) | 8AF0 (B) | RnaseA | PF00074 | P03950 | 28 | 140 | 390 | R | C | UB | |
| 8DZK (A:F) | E. Histolytica RNA lariat debranching enzyme | 5-mer RNA | 5K71 (A) | 8DZK (A) | Metallophos | PF00149 | C4M1P9 | 7 | 234 | 1255 | R | D | UB | |
| 8DZK (A:F) | E. Histolytica RNA lariat debranching enzyme | 5-mer RNA | 5K71 (A) | 8DZK (A) | Dbr1_C | PF20890 | C4M1P9 | 268 | 353 | 0 | R | D | UB | |
| 8EDJ (A:R) | M. Mulatta APOBEC3G | ssRNA | 6P3X (A) | 8EDJ (A) | SNAD4 | PF18750 | Q7YR23 | 21 | 160 | 1549 | F | D | UB | |
| 8EDJ (A:R) | M. Mulatta APOBEC3G | ssRNA | 6P3X (A) | 8EDJ (A) | NAD2 | PF18782 | Q7YR23 | 188 | 370 | 190 | F | D | UB | |
| 8EY8 (A:B) | H. sapiens LARP1 | polyA | 7SOO (A) | 8EY8 (A) | LA domain | PF05383 | Q6PKG0 | 19 | 75 | 0 | R | D | UB | |
| 8H1B (AB:CD) | S. aureus MnmM | anticodon stem loop of tRN | 8H1A (AB) | 8H1B (A) | rRNA_methylase | PF06962 | Q2FXG9 | 47 | 184 | 1255 | S | A | UB | |
| 8H1B (AB:CD) | S. aureus MnmM | anticodon stem loop of tRN | 8H1A (AB) | 8H1B (B) | rRNA_methylase | PF06962 | Q2FXG9 | 47 | 184 | 1388 | S | A | UB | |
| 8JOZ (A:B) | E. coli CmoM | tRNA-Ser | 4HTF:A | 8JOZ (A) | Methyltransferase dom | PF13847 | P36566 | 61 | 612 | 1591 | R | A | UB | |
| 8OIV (A:D) | Monkeypox visus VP39 | mRNAs | 1VPT (A) | 8OIV (A) | PARP_regulatory | PF01358 | A0A7H0DN74 | 5 | 296 | 1627 | R | D | UB | |
| 8PE3 (AB:C) | S. thermophilus CRISPR Csm6' | mRNA | 8PCW (AB) | 8PE3 (A) | Cas_Csm6_CARF | PF22208 | A0A0A7HFE6 | 65 | 168 | 1332 | F | D | UB | |
| 8PE3 (AB:C) | S. thermophilus CRISPR Csm6' | mRNA | 8PCW (AB) | 8PE3 (A) | Cas_Csm6_HEPN | PF09659 | A0A0A7HFE6 | 236 | 308 | 0 | F | D | UB | |
| 8PE3 (AB:C) | S. thermophilus CRISPR Csm6' | mRNA | 8PCW (AB) | 8PE3 (B) | Cas_Csm6_CARF | PF22208 | A0A0A7HFE6 | 65 | 168 | 1329 | F | D | UB | |
| 8PE3 (AB:C) | S. thermophilus CRISPR Csm6' | mRNA | 8PCW (AB) | 8PE3 (B) | Cas_Csm6_HEPN | PF09659 | A0A0A7HFE6 | 236 | 308 | 0 | F | D | UB | |
| 8SH5 (HL:R) | M. Musculus Fab BL3-6K170A | CITE RNA | 4DKE:HL | 8SH5 (H) | Immunoglobulin C1-set | PF07654 | NA | 133 | 213 | 0 | S | C | UB | |
| 8SH5 (HL:R) | M. Musculus Fab BL3-6K170A | CITE RNA | 4DKE:HL | 8SH5 (H) | Immunoglobulin V-set | PF07686 | NA | 15 | 12 | 0 | S | C | UB | |
| 8SH5 (HL:R) | M. Musculus Fab BL3-6K170A | CITE RNA | 4DKE:HL | 8SH5 (L) | Immunoglobulin C1-set | PF07654 | NA | 116 | 202 | 0 | S | C | UB | |
| 8SH5 (HL:R) | M. Musculus Fab BL3-6K170A | CITE RNA | 4DKE:HL | 8SH5 (L) | Immunoglobulin V-set | PF07686 | NA | 7 | 107 | 340 | S | C | UB | |
| 8TG4 (A:C) | A. pernix Tpt1 | 2'-OH RNA | 8TG3:A | 8TG4 (A) | PTS_2-RNA | PF01885 | Q9YFP5 | 22 | 184 | 527 | R | D | UB |
aFour-letter PDB code of the protein-RNA complexes used in
the benchmark with the chain id of the protein and the RNA molecules in the
parenthesis. For structures solved by NMR (shown
in bold font) the first model was used for the structural alignment. Symmetry
related chains are primed (For example, A' and B' in 3HL2). If
the Unbound RNA structure is taken from another complex they are marked with
* (For example, in 3I9C nucleotides from 1080 to 1129 are considered).
bProtein name and chain in a protein-RNA complex.
cRNA name and chain in a protein-RNA complex.
dUnbound protein name and chain.
eUnbound RNA name and chain.
fDomain mapped to protein chain.
gPfam domain name
hPfam domain ID
iUniprot ID. jPfam domain start position in a PDB chain.
kPfam domain end position in a PDB chain.
lBuried Surface area calculated for pfam doamin interacting with RNA.
mFlexible categores from PRDBv3.0: rigid (R); semi-flexible (S); full-flexible (F). nStructural classes from PRDBv3.0: complexes with tRNA (A); complexes with rRNA (B); complexes with duplex RNA (C); complexes with single-stranded RNA. oDocking cases from PRDBv3.0: Unbound-Unbound (UU); Unbound-Bound (UB); Bound-Unbound (BU).