Click here to download the PRDBv3.0 dataset.
Each folder contains the protein-RNA complex, the unbound structure of protein and/or RNA (wherever available) along with the transformed coordinates of unbound protein and/or RNA subunits superposed with the bound subunits. The subunits have been filtered and only chains of interest are retained in the PDB files.
Dataset of protein-RNA binding affinity benchmark.
Pfam domain details on protein-RNA docking benchmark version 3.0.
Protein-RNA docking benchmark dataset GitHub repository.
Table S1: A non-redundant docking benchmark dataset of protein-RNA complexes.
|
Bounda |
Unbound (PDB ID)a |
BSA (Å)b |
RMSD (Å) |
GDT_TS |
LGA_S |
Category |
|||||||
|
PDB ID |
Protein |
RNA |
Protein |
RNA |
Cα-rmsdc |
P-rmsdd |
i-rmsde |
||||||
|
Cα |
P |
Cα+P |
|||||||||||
|
I. Unbound-Unbound cases (27) |
|||||||||||||
|
(A) Complexes with tRNA (13) |
|||||||||||||
|
1ASY (A:R) |
S.
cerevisiae aspartyl-tRNA synthetase |
tRNA-Asp |
1EOV (A) |
2TRA (A) |
4430 |
1.5 |
4.9 |
1.3 |
3.3 |
2.3 |
85.4 |
92.8 |
R |
|
1B23 (P:R) |
T.
aquaticus
EF-TU |
E.
coli
tRNA-Cys |
1TUI (A) |
1U0B* (A) |
2616 |
10 |
7.2 |
13.3 |
13 |
13.2 |
50.3 |
47.7 |
F |
|
1C0A (A:B) |
E.
coli aspartyl-tRNA
synthetase |
tRNA-Asp
|
1EQR (A) |
1EFW* (C) |
4504 |
1.6 |
1.8 |
1.6 |
1.8 |
1.7 |
84.0 |
92.0 |
S |
|
1QTQ (A:B) |
E.
coli
glutaminyl-tRNA synthetase |
tRNA-Gln |
1NYL (A) |
3KNH* (Y) |
5202 |
1.6 |
4.8 |
1.8 |
6.4 |
4.0 |
86.7 |
93.0 |
S |
|
2BTE (A:B) |
T.
thermophilus leucyl-tRNA synthetase |
tRNA-Leu
|
1OBC (A) |
2NQP* (F) |
3430 |
1.2 |
4.6 |
1.3 |
4.1 |
2.5 |
77.1 |
68.4 |
R |
|
2DRB (A:B) |
A.
fulgidus
CCA-adding enzyme |
tRNAmini
CCA |
1UET (A) |
3Q1Q* (C) |
3198 |
1.1 |
3.4 |
1.8 |
4.2 |
2.5 |
86.8 |
87.8 |
S |
|
2FMT (A:C) |
E.
coli methionyl-tRNAfmet
transformylase |
tRNA-fmet |
1FMT (A) |
3CW6 (A) |
2940 |
1.2 |
2.3 |
0.9 |
2.5 |
1.7 |
91.2 |
96.1 |
R |
|
2ZZM (A:B) |
M.
jannaschii tRNA (guanine(37)-N1)-methyltransferase Trm5b |
tRNA-Leu
|
2YX1 (A) |
1WZ2* (C) |
4523 |
15.1 |
4.6 |
20 |
6.4 |
12.9 |
74.5 |
73.9 |
F |
|
3HL2
(AA'BB':E) |
H.
sapiens selenium
transferase |
tRNA-Sec |
3BC8
(AA'A''A''') |
3RG5 (A) |
2186 |
0.6 |
5.2 |
1.3 |
6.0 |
4.3 |
98.0 |
98.9 |
R |
|
3VJR (A:B) |
E.
coli peptidyl-tRNA
hydrolase |
tRNA
CCA-acceptor |
2PTH (A) |
1NJM* (5) |
1354 |
0.8 |
3.7 |
0.8 |
3.8 |
2.0 |
95.9 |
97.9 |
R |
|
5X6B
(IJEF:P) |
M.
jannaschii SepCysE-SepCysS |
tRNA-Cys |
3WKR
(ABCD) |
2ZZN* (C) |
4240 |
0.6 |
3.2 |
1.2 |
6.4 |
3.5 |
99.1 |
99.6 |
R |
|
6LVR (C:D) |
A.
thaliana
PRORP1 |
yeast
tRNA-Phe |
4G24 (A) |
1I9V (A) |
1055 |
3.4 |
1.3 |
4.4 |
1.1 |
4.0 |
70.3 |
67.3 |
F |
|
7YSE
(AC:E) |
E.
coli
Glycine--tRNA |
tRNA-Gly |
7EIV (AC) |
7F36* (E) |
9045 |
3.5 |
6.0 |
4.6 |
5.9 |
4.7 |
82.4 |
80.6 |
F |
|
(B) Ribosomal proteins (4) |
|||||||||||||
|
1DFU
(P:MN) |
E.
coli ribosomal
protein L25 |
5s
rRNA |
1B75 (A) |
364D (CB) |
1690 |
3.0 |
5.3 |
3.0 |
4.4 |
3.7 |
73.4 |
70.4 |
F |
|
1FEU
(A:BC) |
T.
thermophilus ribosomal protein L5 |
5s
rRNA |
2J01 (Z) |
364D (BC) |
1595 |
2.1 |
3.3 |
2.4 |
2.8 |
2.6 |
82.1 |
80.7 |
S |
|
1MMS (A:C) |
T.
maritima
ribosomal protein L11 |
23S
rRNA fragment |
2K3F (A) |
3I9C*
(A:1080-1129) |
2455 |
3.5 |
1.6 |
4.1 |
1.6 |
3.3 |
65.2 |
62.3 |
F |
|
3IEV (A:D) |
A.
aeolicus
GTPase era |
16S
rRNA |
7C1O (A) |
1SDR (B) |
2273 |
0.5 |
7.6 |
0.5 |
8.4 |
4.5 |
98.7 |
99.5 |
R |
|
(C) Duplex RNA (6) |
|||||||||||||
|
1OOA (A:C) |
M.
musculus NF-kappaB
p50 |
aptamer
RNA |
1LE5 (B) |
2JWV* (A) |
1909 |
6.2 |
6.7 |
5.5 |
7.0 |
6.3 |
64.1 |
62.7 |
F |
|
1R3E (A:C) |
T.
maritime pseudouridine
synthase TruB |
tRNA
fragment |
1ZE1 (A) |
1EHZ
(A:49-65) |
3680 |
2.0 |
4.9 |
3.3 |
4.9 |
3.6 |
82.9 |
76.4 |
F |
|
2R8S
(LH:R) |
M.
musculus synthetic
FAB |
ribozyme |
2HFF (AB) |
1HR2 (A) |
2510 |
1.6 |
4.3 |
2.9 |
2.1 |
2.5 |
87.1 |
93.8 |
S |
|
3SNP (A:C) |
O.
cuniculus iron regulatory protein 1 |
ferritin
H IRE RNA |
2B3Y (A) |
1AQO* (A) |
2872 |
0.7 |
3.8 |
14.5 |
3.3 |
12.8 |
44.2 |
40.2 |
F |
|
2OZB
(AB:C) † |
H.
sapiens
Ribonucleoprotein |
U4snRNA |
2JNB (A) |
2XEB (A) |
2569 |
1.9 |
11.0 |
1.9 |
13.0 |
19.0 |
80.7 |
90.3 |
S |
|
7P0V (A:B) |
H.
sapiens
SF3A1 ubiquitin-like domain |
U1
snRNA SL-4 |
7P08 (A) |
8ID2* (C) |
1210 |
1.5 |
1.1 |
1.7 |
0.9 |
1.4 |
87.6 |
94.3 |
S |
|
(D) Single-stranded RNA (4) |
|||||||||||||
|
1JBS (A:C) |
A.
restrictus restrictocin |
SRD
RNA analogue |
1AQZ (A) |
1Q9A (A) |
1310 |
0.7 |
3.4 |
0.6 |
3.2 |
1.9 |
97.0 |
98.9 |
R |
|
1WSU (A:E) |
M.
thermoacetica elongation factor Sel B |
SECIS
RNA |
1LVA (A) |
2RLU (A) |
940 |
0.7 |
4.2 |
0.5 |
1.1 |
0.8 |
98.0 |
98.5 |
R |
|
1ZBH
(AD:E) |
H.
sapiens exonuclease
ERI1 |
histone
mRNA |
1ZBU (AD) |
1JU7 (A) |
1760 |
0.6 |
3.6 |
0.6 |
3.4 |
2.0 |
49.6 |
49.8 |
R |
|
2BH2 (A:C) |
E.
coli methyltransferase
Rum A |
23S
rRNA |
1UWV (A) |
1JZX*
(A:1915-1951) |
4491 |
1.4 |
9.8 |
0.7 |
11.0 |
6.0 |
86.0 |
93.5 |
R |
|
II. Unbound-Bound (160) |
|||||||||||||
|
(A) Complexes with tRNA (25) |
|||||||||||||
|
1F7U (A:B) |
S.
cerevisiae arginyl-tRNA synthetase |
tRNA-Arg |
1BS2 (A) |
5767 |
2.0 |
2.2 |
79.2 |
75.1 |
S |
||||
|
1H3E
(AA':B) |
T.
thermophilus tyrosyl-tRNA synthetase |
tRNA-Tyr |
1H3F (AB) |
3758 |
7.7 |
4.5 |
68.3 |
62.6 |
F |
||||
|
1H4S
(AB:T) |
T.
thermophilus prolyl-tRNA synthetase |
tRNA-Pro |
1HC7 (AB) |
2480 |
1.0 |
0.9 |
88.6 |
94.5 |
R |
||||
|
1J1U
(AA':B) |
M.
jannaschii tyrosyl-tRNA synthetase |
tRNA-Tyr |
1U7D (AB) |
2240 |
1.3 |
0.8 |
73.5 |
71.6 |
R |
||||
|
1N78 (A:C) |
T.
thermophilus glutamyl-tRNA synthetase |
tRNA-Glu |
1J09 (A) |
4510 |
1.9 |
1.4 |
86.4 |
92.4 |
R |
||||
|
1QF6 (A:B) |
E.
coli
threonyl-tRNA synthetase |
tRNA-Thr |
1EVL (A) |
4602 |
0.8 |
0.7 |
96.6 |
98.5 |
R |
||||
|
1SER
(AB:T) |
T.
thermophilus seryl-tRNA synthetase |
tRNA-Ser |
1SES (AB) |
2290 |
1.7 |
2.4 |
91.7 |
95.9 |
S |
||||
|
1U0B (B:A) |
E.
coli
cysteinyl-tRNA synthetase |
tRNA-Cys |
1LI5 (B) |
4560 |
0.7 |
1.0 |
97.7 |
98.9 |
R |
||||
|
1VFG (B:D) |
A.
aeolicus CCA-adding
enzyme |
tRNA |
4WBY (A) |
1664 |
1.6 |
1.4 |
90.8 |
95.1 |
R |
||||
|
2AZX
(AA':C) |
H.
sapiens
tryptophanyl-tRNA synthetase |
tRNA-Trp |
1R6U (AB) |
2130 |
0.8 |
0.6 |
91.5 |
96.5 |
R |
||||
|
2FK6 (A:R) |
B.
subtilis RNase
Z |
tRNA-Thr |
1Y44 (A) |
1530 |
0.7 |
0.8 |
97.6 |
98.8 |
R |
||||
|
3ADB (A:C) |
M.
jannaschii O-phosphoseryl-tRNA kinase |
tRNA-Sec |
3A4M (A) |
3099 |
22.4 |
27.3 |
72.8 |
70.2 |
F |
||||
|
3AMT (A:B) |
A.
fulgidus agmatinylcytidine
synthetase TiaS |
tRNA-Ile |
3AU7 (A) |
3821 |
0.8 |
0.7 |
95.6 |
93.6 |
R |
||||
|
4YCP (A:B) |
E.
coli tRNA-dihydrouridine
synthase C |
tRNA-Trp |
4BFA (A) |
2151 |
0.4 |
6.8 |
99.8 |
99.9 |
F |
||||
|
4YVJ
(AB:C) |
H.
influenzae tRNA methyltransferase D |
tRNA |
3AXZ (AA') |
2313 |
0.7 |
1.3 |
96.0 |
98.4 |
R |
||||
|
5HR7 (A:D) |
E.
coli
RNA methyltransferase RlmN |
tRNA-Glu |
3RFA (A) |
3450 |
1.4 |
1.3 |
93.7 |
96.7 |
R |
||||
|
5B63 (A:B) |
E.coli
arginyl-tRNA synthetase |
tRNA-Arg |
5YYM (A) |
|
3360 |
1.2 |
1.5 |
85.6 |
90.9 |
S |
|||
|
5T8Y (B:X) |
B.
subtilis subsp. epoxyqueuosine reductase |
anticodon
stem loop of tRNA-Tyr |
5D08 (A) |
697 |
0.4 |
0.3 |
96.0 |
96.6 |
R |
||||
|
5WT1 (A:C) |
P.
abyss
Trm5a |
tRNA
Phe |
5HJI (A) |
4824 |
11.5 |
12.1 |
69.6 |
73.2 |
F |
||||
|
5ZW4 (A:D) |
B.
subtilis subsp. TrmR |
tRNA
fragment |
5ZW3 (A) |
762 |
0.6 |
0.9 |
98.2 |
99.3 |
R |
||||
|
7E8O
(AB:X) |
P.
bacterium
PRORP |
pre-tRNA-His |
7E8K (AB) |
801 |
1.8 |
1.0 |
89.0 |
92.6 |
R |
||||
|
7K98
(ABDE:CF) |
M.
tuberculosis PheRS |
tRNA-Phe |
7DAW
(AA'BB') |
7115 |
1.5 |
7.9 |
90.4 |
94.0 |
F |
||||
|
7MJW (A:M) |
B.
uniformis
methylated MiaB |
tRNA |
7MJZ (A) |
2677 |
1.4 |
1.5 |
88.2 |
93.9 |
S |
||||
|
8H1B (A:C) |
S.
aureus
rRNA methylase YtqB |
tRNA |
8H1A (A) |
1397 |
0.9 |
1.9 |
95.0 |
97.6 |
S |
||||
|
8JOZ (A:B) |
E.
coli
CmoM |
tRNA-Ser |
4HTF (A) |
1906 |
0.6 |
1.1 |
94.4 |
95 |
R |
||||
|
(B) Ribosomal proteins (4) |
|||||||||||||
|
1G1X
(ABC:DE) † |
T.
thermophilus ribosomal proteins S6, S15, S18 |
16S
rRNA |
1CQM (A) |
4945 |
0.9 |
1.1 |
93.1 |
95.1 |
R |
||||
|
1SDS
(C:FF') |
M.
jannaschii 50S ribosomal protein L7Ae |
box
H/ACA sRNA |
1XBI (A) |
1200 |
0.3 |
0.4 |
100.0 |
100.0 |
R |
||||
|
2HW8 (A:B) |
T.
thermophilus ribosomal protein L1 |
mRNA |
1AD2 (A) |
2401 |
6.7 |
5.1 |
64.6 |
47.4 |
F |
||||
|
5WTY (A:C) |
S.
cerevisiae nucleolar protein 9 |
18s
rRNA |
5SVD (B) |
3205 |
2.5 |
2.6 |
75.8 |
80.2 |
S |
||||
|
(C) Duplex RNA (51) |
|||||||||||||
|
1MSW (D:R) |
Phage
T7 RNA polymerase |
RNA
transcript |
1ARO (P) |
1830 |
3.5 |
3.5 |
57.1 |
54.1 |
F |
||||
|
1N35
(A:BC) |
Reovirus
polymerase |
dsRNA |
1MUK (A) |
3240 |
0.5 |
0.9 |
99.3 |
99.7 |
R |
||||
|
1Q2R
(AB:E) |
Z.
mobilis guanine
transglycosylase |
20-mer
tRNA fragment |
1R5Y (AA') |
3006 |
0.6 |
1.6 |
98.0 |
99.0 |
S |
||||
|
1WNE
(A:BC) |
Foot-and-mouth
disease virus polymerase |
template-primer
RNA decanucleotide |
1U09 (A) |
3080 |
0.7 |
0.6 |
97.2 |
99.0 |
R |
||||
|
1YVP
(B:EFH) |
F.
laevis Ro
autoantigen |
Y RNA |
1YVR (A) |
4207 |
1.4 |
1.3 |
90.6 |
95.2 |
R |
||||
|
1ZBI
(A:CD) |
B.
halodurans RNase H |
A form
RNA |
1ZBF (A) |
1675 |
0.6 |
0.6 |
98.7 |
99.5 |
R |
||||
|
2AZ0
(AB:CD) |
Flock
house virus B2 |
siRNA |
2B9Z (AB) |
2264 |
1.3 |
1.0 |
85.5 |
93.3 |
R |
||||
|
2BGG
(A:PQ) |
A.
fulgidus
PIWI |
siRNA |
1W9H (A) |
2240 |
0.9 |
0.8 |
96.5 |
98.2 |
R |
||||
|
2EZ6
(AB:CD) |
A.
aeolicus RNase
III |
28-mer
RNA |
1JFZ (AB) |
|
5193 |
1.0 |
0.8 |
95.5 |
84.9 |
R |
|||
|
2F8S
(AB:CD) |
A.
aeolicus
argonaute |
siRNA |
1YVU (A) |
990 |
1.9 |
1.5 |
77.4 |
78.3 |
S |
||||
|
2GJW
(AB:EFH) |
A.
fulgidus splicing
endonuclease |
bulge-helix-bulge
RNA |
1R0V (AB) |
3243 |
1.0 |
1.0 |
83.0 |
91.7 |
R |
||||
|
2GXB
(A:EF) |
H.
sapiens Z
alpha domain of adenosine deaminase |
dsRNA |
1QGP (A) |
768 |
1.1 |
0.7 |
87.9 |
90.9 |
R |
||||
|
2QUX
(AB:C) |
Pseudomonas
phage PP7 coat protein |
hairpin
RNA |
2QUD (AB) |
1754 |
0.9 |
0.5 |
96.9 |
98.4 |
R |
||||
|
2Y8W (A:B) |
T.
thermophilus endoribonuclease Cse3 |
hairpin
RNA |
1WJ9 (A) |
3258 |
1.1 |
3.1 |
95.5 |
97.3 |
F |
||||
|
2ZKO
(AB:CD) |
NS1
protein of influenza A |
A-form
dsRNA |
2Z0A (AB) |
2466 |
0.6 |
0.8 |
97.7 |
98.8 |
R |
||||
|
3A6P
(AC:DE) |
H.
sapiens exp-5:Ran GTP |
pre-microRNA |
5YU6 (AB) |
4223 |
1.2 |
1.4 |
91.8 |
96.4 |
R |
||||
|
3BSN
(A:PT) |
Norwalk
virus polymerase |
synthetic
RNA |
1SH3 (A) |
3111 |
1.3 |
1.9 |
90.9 |
95.2 |
S |
||||
|
3DD2 (H:B) |
H.
sapiens thrombin |
26-mer
RNA |
1JOU (D) |
1822 |
0.6 |
0.5 |
96.5 |
98.1 |
R |
||||
|
3EQT
(AB:CD) |
H.
sapiens helicase
DHX58 |
dsRNA |
2W4R (AA') |
2705 |
1.2 |
1.2 |
47.9 |
42.5 |
R |
||||
|
3FTE
(A:CD) |
A.
aeolicus methyltransferase
KsgA |
rRNA |
3FTD (A) |
836 |
1.4 |
1.1 |
89.7 |
94.9 |
R |
||||
|
3KS8
(AB:EF) |
R.
ebolavirus polymerase cofactor VP35 |
dsRNA |
3KS4 (AB) |
1663 |
0.6 |
0.4 |
49.8 |
50.1 |
R |
||||
|
3MOJ (B:A) |
B.
subtilis helicase
dbpA |
E.coli 23S
rRNA fragment |
2G0C (A) |
1758 |
1.0 |
1.0 |
94.5 |
97.6 |
R |
||||
|
3O3I (X:A) |
H.
sapiens Hiwi1
PAZ domain |
piRNA |
2L5C (A) |
923 |
2.1 |
2.7 |
79.0 |
84.5 |
S |
||||
|
3OIJ
(AB:C) |
S.
cerevisiae methyltransferase |
SSU
rRNA |
3OII (AB) |
2070 |
0.8 |
1.7 |
97.0 |
98.5 |
S |
||||
|
3OL6
(A:BCD) |
Poliovirus
polymerase |
synthetic
RNA |
1RA6 (A) |
4174 |
0.8 |
1.1 |
94.9 |
97.8 |
R |
||||
|
3RW6 (A:H) |
H.
sapiens nuclear
RNA export factor 1 |
CTE
RNA |
3RW7 (A) |
2699 |
13.5 |
19.0 |
66.4 |
64.4 |
F |
||||
|
3ZC0
(AA'BB'CC'DD':MM') |
A.
fulgidus C3PO |
duplex
RNA |
3ZC1
(ABCDEFGH) |
2324 |
0.5 |
0.5 |
98.6 |
99.2 |
R |
||||
|
4ERD
(AB:CD) |
T.
thermophila p65 C-terminal domain |
stem
IV of telomerase RNA |
4EYT (AB) |
3280 |
1.5 |
1.2 |
47.0 |
46.5 |
R |
||||
|
4FVU
(A:BC) |
Lassa
virus exonuclease |
dsRNA |
3Q7C (A) |
1240 |
1.0 |
0.7 |
97.2 |
98.5 |
R |
||||
|
4IG8
(A:BC) |
H.
sapiens oligoadenylate
synthetase 1 |
dsRNA |
1PX5 (A) |
2914 |
2.4 |
2.8 |
79.0 |
74.4 |
S |
||||
|
4ILL
(AB:RC) |
S.
solfataricus endoribonuclease Cas6 |
CRISPR
RNA |
4ILR (AA') |
7074 |
0.9 |
0.9 |
96.3 |
98.1 |
R |
||||
|
4ZT0 (A:B) |
S.
pyogenes CRISPR-associated
endonuclease Cas9 |
single-guide
RNA |
4CMP (A) |
10845 |
29.6 |
22 |
45.6 |
43.1 |
F |
||||
|
5ED1
(A:BC) |
H.
sapiens ADAR2 |
S.
cerevisiae dsRNA |
1ZY7 (A) |
2403 |
1.1 |
2.3 |
95.4 |
97.5 |
S |
||||
|
5F5H (A:C) |
M.
musculus Roquin-1 |
Ox40
3'-UTR |
4QI0 (A) |
1618 |
0.5 |
0.6 |
99.2 |
99.6 |
R |
||||
|
5WTK (A:B) |
L.
shahii CRISPR-associated
endoribonuclease C2c2 |
crRNA |
5WTJ (A) |
|
8811 |
4.9 |
4.0 |
60.5 |
65.2 |
F |
|||
|
5ZQ8 (A:D) |
S.
pneumoniae RlmCD |
23S
rRNA U747 stemloop |
5XJ1 (A) |
1992 |
1.5 |
1.2 |
86.4 |
93.7 |
R |
||||
|
6D12 (B:C) |
H.
sapiens xRRM domain of human Larp7 |
7SK
stem-loop 4 RNA |
5KNW (A) |
1428 |
2.1 |
1.6 |
79.1 |
88.2 |
S |
||||
|
6DCB (A:B) |
H.
sapiens
methylphosphate capping enzyme |
5' end
of 7SK RNA |
5UNA (A) |
697 |
0.7 |
0.3 |
95.0 |
95.8 |
R |
||||
|
6FQ3 (A:B) |
D.
rerio E3
ubiquitin-protein ligase TRIM71 |
lin-29A
5'UTR |
6FPT (A) |
986 |
7.9 |
2.0 |
72.5 |
74.7 |
S |
||||
|
6SY4
(AB:C) |
E.
coli TetR |
TetR-binding
aptamer K1 |
3ZQI (AB) |
1702 |
1.7 |
2.0 |
82.1 |
91.0 |
S |
||||
|
6PZQ
(AB:IJ) |
HRSV
matrix M2-1 |
Gene-End
RNA |
6G0Y (AC) |
668 |
0.9 |
0.5 |
97.6 |
99.2 |
R |
||||
|
6RTI (A:X) |
H.
sapiens
GCPII |
A9gRNA
aptamer |
2C6C (A) |
3147 |
0.4 |
0.6 |
99.6 |
99.9 |
R |
||||
|
6ZDP (A:B) |
C.
tropicalis telomerase reverse transcriptase |
TWJ
fragment of telomeric RNA |
6ZD6 (A) |
2629 |
4.1 |
8.4 |
60.7 |
62.0 |
F |
||||
|
7KFN
(AD:BC) |
H.
sapiens
ADAR2 |
Gli1
8AZ 23mer dsRNA |
1ZY7 (AB) |
2724 |
0.9 |
1.6 |
97.2 |
98.6 |
S |
||||
|
7KKV (A:B) |
A.
halodurans OapB protein |
OLE
RNA target |
7K9B (A) |
|
1365 |
0.7 |
0.7 |
88.3 |
89.9 |
R |
|||
|
7OG0
(A:EE') |
H.
influenzae SapA |
dsRNA |
8TV8 (A) |
|
597 |
3.0 |
2.1 |
65.4 |
59.7 |
S |
|||
|
7OM6
(A:DF) |
T.
asigna
virus RdRP domain |
RNA
oligonucleotide |
7OM2 (A) |
6642 |
0.9 |
1.4 |
96.6 |
98.1 |
R |
||||
|
7XD8
(A:BC) |
Dengue
virus 2 NS5 |
30-mer
RNA |
6KR2 (A) |
3539 |
3.7 |
5.2 |
61.5 |
64.8 |
F |
||||
|
7XWZ
(A:CD) |
SARS-CoV-2
N-NTD
nucleoprotein |
dsRNA |
7VNU (A) |
811 |
1.0 |
2.2 |
96.9 |
98.1 |
S |
||||
|
7ZLQ
(A:DE) |
H.
Sapiens
ADAR1-dsRBD3 |
dsRNA |
2MDR (A) |
784 |
1.3 |
0.6 |
79.8 |
83.8 |
R |
||||
|
8AF0
(AB:CD) |
H.
Sapiens
Angiogenin |
dsRNA |
5M9T (AB) |
1068 |
0.7 |
0.4 |
98.8 |
99.4 |
R |
||||
|
(D) Single-stranded RNA (80) |
|||||||||||||
|
1AV6 (A:B) |
Vaccinia
virus cap-specific mRNA methyltransferase |
M7G
capped RNA |
1B42 (A) |
844 |
0.5 |
0.4 |
99.1 |
99.6 |
R |
||||
|
1C9S
(L:W1-7) |
G.
stearothermophilus TRAP |
ssRNA |
2EXT (A) |
1027 |
0.3 |
0.2 |
100.0 |
100.0 |
R |
||||
|
1CVJ (A:M) |
H.
sapiens poly(A)-binding
protein |
polyA |
4F25 (A) |
2822 |
2.7 |
3.9 |
93.4 |
93.9 |
F |
||||
|
1G2E (A:B) |
H.
sapiens RRM
domain of the HuD protein |
class
II ARE fragment |
4EGL (A) |
2776 |
0.9 |
0.6 |
49.8 |
49.8 |
R |
||||
|
1K8W (A:B) |
E.
coli pseudouridine
synthase B |
T
stem-loop RNA |
1R3F (A) |
2973 |
1.9 |
1.3 |
80.8 |
90.3 |
R |
||||
|
1KQ2
(ABHIKM:R) |
S.
aureus Hfq |
7-mer
RNA |
1KQ1
(ABHIKM) |
3026 |
0.6 |
0.5 |
81.9 |
91.8 |
R |
||||
|
1M5O (C:B) |
H.
sapiens U1
Snp A |
hairpin
ribozyme |
1OIA (A) |
1770 |
1.2 |
0.9 |
96.6 |
98.1 |
R |
||||
|
1M8V
(AM:O) |
P.
abyssi
Sm |
uridine
heptamer |
1H64 (AM) |
1290 |
0.6 |
0.4 |
62.2 |
61.2 |
R |
||||
|
1M8W
(A:CE) |
H.
sapiens pumilio-homology
domain |
Nre1-19
RNA |
1M8Z (A) |
2110 |
0.8 |
0.7 |
90.9 |
96.0 |
R |
||||
|
1UVI (A:D) |
phi6
RNA polymerase |
6-mer
RNA |
1HHS (A) |
1814 |
0.2 |
0.2 |
100.0 |
100.0 |
R |
||||
|
1WPU (A:C) |
B.
subtilis HutP
antitermination protein |
hut
mRNA |
1WPV (A) |
1360 |
0.2 |
0.2 |
100.0 |
100.0 |
R |
||||
|
2A8V (B:E) |
E.
coli RHO |
Cytosine
rich RNA |
1A8V (B) |
720 |
1.0 |
1.6 |
94.7 |
97.7 |
S |
||||
|
2ASB (A:B) |
M.
tuberculosis Nus A antiterminator |
BoxC
rRNA |
1K0R (A) |
2320 |
1.1 |
0.8 |
91.8 |
96.4 |
R |
||||
|
2GIC (A:R) |
VSV
nucleocapsid |
viral
genomic RNA |
2QVJ (A) |
2000 |
1.3 |
0.9 |
91.9 |
95.7 |
R |
||||
|
2IX1 (A:B) |
E.
coli RNase
II |
polyA |
2IX0 (A) |
4160 |
1.6 |
0.9 |
86.2 |
93.3 |
R |
||||
|
2JEA
(AB:C) |
S.
solfataricus exosome |
substrate
RNA |
2JE6 (AB) |
1533 |
0.3 |
0.3 |
99.8 |
99.9 |
R |
||||
|
2JLU (A:C) |
Dengue
virus serine protease subunit NS3 |
ssRNA |
2JLQ (A) |
1925 |
2.1 |
2.8 |
74.3 |
78.1 |
S |
||||
|
2PY9 (B:E) |
H.
sapiens poly(rC)-binding
protein 2 |
human
telomeric RNA |
2JZX
(A:1-73) |
1060 |
1.4 |
1.6 |
85.5 |
92.0 |
R |
||||
|
2Q66 (A:X) |
S.
cerevisiae poly(A) polymerase |
polyA |
2HHP (A) |
1811 |
1.9 |
2.1 |
85.0 |
91.5 |
S |
||||
|
2R7R (A:X) |
Rotavirus
polymerase VP1 |
RNA |
2R7Q (A) |
1955 |
0.2 |
1.9 |
98.7 |
99.3 |
S |
||||
|
2XGJ (A:C) |
S.
cerevisiae Mtr4 |
polyA |
4U4C (A) |
1389 |
4.1 |
3.1 |
71.5 |
65.5 |
F |
||||
|
2XNR (A:C) |
S.
cerevisiae Nab3-RRM |
UCUU
recognition sequence |
2XNQ (A) |
926 |
1.0 |
1.2 |
94.3 |
97.4 |
R |
||||
|
2XZO (A:D) |
H.
sapiens Upf1
helicase |
polyU |
2XZP (A) |
2006 |
6.2 |
5.0 |
57.2 |
54.2 |
F |
||||
|
3AEV (B:C) |
P.
horikoshii Dim2p |
P.
horikoshii 16S rRNA fragment |
2E3U (A) |
2416 |
0.7 |
0.5 |
97.4 |
99.0 |
R |
||||
|
3BX2 (A:C) |
S.
cerevisiae PUF4 |
3' UTR
binding sequence |
3BWT (A) |
2467 |
0.6 |
0.5 |
98.5 |
99.3 |
R |
||||
|
3D2S (A:E) |
H.
sapiens
MBNL1 ZnF3/4 |
pre-mRNA |
3D2Q (A) |
569 |
0.8 |
0.6 |
97 |
98.7 |
R |
||||
|
3MDG
(AB:C) |
H.
sapiens
CFI(m)25 |
pre-mRNA |
3BAP (AA') |
1069 |
0.5 |
0.9 |
96.5 |
98.1 |
R |
||||
|
3NMR (A:B) |
H.
sapiens
CUG-binding protein 1 |
UGU-rich
mRNA |
2DHS (A) |
1096 |
2.7 |
2.2 |
43.0 |
39.7 |
S |
||||
|
3O8C (A:C) |
HCV
NS3 helicase |
polyU |
3O8B (A) |
1909 |
1.0 |
1.1 |
94.6 |
97.5 |
R |
||||
|
3PF4 (B:R) |
B.
subtilis CspB |
ssRNA |
1CSP (A) |
963 |
0.5 |
0.4 |
98.5 |
99.4 |
R |
||||
|
3QJJ (A:Q) |
P.
horikoshii RAMP Protein |
CRISPR
repeat RNA |
3UFC (X) |
3191 |
1.0 |
1.0 |
96 |
98.3 |
R |
||||
|
3RC8 (A:E) |
H.
sapiens
helicase SUPV3L1 |
RNA
fragment |
3RC3 (A) |
1471 |
1.1 |
0.8 |
92.3 |
96.3 |
R |
||||
|
4E78
(A:PT) |
HCV
polymerase |
RNA
primer-template pair |
4E76 (A) |
2100 |
0.7 |
0.8 |
98.4 |
99.4 |
R |
||||
|
4H5P
(AB:E) |
Rift
valley fever virus nucleocapsid |
polyU |
3LYF (AB) |
4482 |
0.9 |
2.1 |
42.5 |
42.6 |
S |
||||
|
4HOR (A:X) |
H.
sapiens
IFIT |
polyC |
4HOQ (A) |
1747 |
3.1 |
2.4 |
68.7 |
72.5 |
S |
||||
|
4J7M (A:B) |
M.
musculus Dom3Z |
polyU |
4J7N (A) |
1268 |
0.3 |
0.3 |
99.7 |
99.9 |
R |
||||
|
4M59
(AB:CD) |
Z.
mays chloroplast
ppr10 |
psaJ
RNA |
4M57 (AA') |
7842 |
10.5 |
7.1 |
30.1 |
26.1 |
F |
||||
|
4MDX
(AB:C) |
B.
subtilis mRNA
interferase MazF |
mRNA |
1NE8 (AA') |
2127 |
0.7 |
1.6 |
98.4 |
86.4 |
S |
||||
|
4N2Q (A:B) |
B.
distachyon thylakoid assembly 8 |
Zm4
13-mer RNA |
4ME2 (A) |
814 |
2.3 |
1.3 |
78.6 |
82.3 |
R |
||||
|
4QU6 (A:B) |
H.
sapiens
GRSF1 |
synthetic
RNA |
2LMI (A) |
696 |
2.5 |
2.4 |
80.8 |
80.6 |
S |
||||
|
5DET
(AB:PQ) |
H.
sapiens
RBPMS |
CAC
containing ssRNA |
5CYJ (AB) |
2137 |
1.2 |
1.6 |
46.9 |
47.6 |
S |
||||
|
5EIM (A:C) |
S.
pombe
YTH domain of spMmi1 |
synthetic
RNA |
5H8A (A) |
1529 |
0.6 |
1.3 |
98.2 |
99.3 |
R |
||||
|
5ELS
(AC:HI) |
H.
sapiens
KH domain of T-STAR |
synthetic
RNA |
5EL3 (AB) |
2313 |
1.5 |
2.9 |
47.7 |
49.1 |
S |
||||
|
5EX7 (A:B) |
D.
melanogaster Brat NHL domain |
hunchback
mRNA |
1Q7F (A) |
|
1639 |
0.5 |
0.8 |
97.0 |
97.6 |
R |
|||
|
5GXH (A:B) |
H.
sapiens
Gemin5 |
Pre-snRNAs |
5TEE (A) |
1711 |
0.4 |
0.2 |
97.0 |
97.2 |
R |
||||
|
5LTA (A:E) |
T.
thermophila DEAH-box heicase Prp43 |
Synthetic
RNA |
5D0U (A) |
2287 |
2.4 |
2.2 |
72.1 |
76.4 |
S |
||||
|
5SZE (A:C) |
A.
aeolicus
Hfq-RNA |
PolyU |
5SZD (A) |
502 |
1.1 |
0.5 |
94.1 |
95.1 |
R |
||||
|
5V7C (B:C) |
H.
sapiens
LARP1-unique domain DM15 |
5'TOP
motif |
5V87 (A) |
1238 |
0.4 |
0.5 |
96.9 |
97.2 |
R |
||||
|
5W0M (A:H) |
H.
sapiens
TUT7 catalytic module |
PolyU |
5W0B (A) |
1734 |
0.9 |
1.1 |
93.4 |
97.2 |
R |
||||
|
5WWX (A:C) |
H.
sapiens
KH2 domain of MEX-3C |
5-mer
RNA |
5WWZ (A) |
1380 |
0.8 |
0.9 |
92.9 |
96.8 |
R |
||||
|
5ZSC (A:C) |
M.
mulatta
toll-like receptor 7 |
CCUUCA
RNA |
6IF5 (A) |
1227 |
0.5 |
0.5 |
99.7 |
99.8 |
R |
||||
|
6A4E (A:B) |
C.
psychrerythraea oligoribonuclease |
U-rich
RNA |
6A4D (A) |
759 |
0.5 |
0.4 |
98.6 |
99.5 |
R |
||||
|
6A6J (A:B) |
D.
rerio
cold shock domain of Ybx1 |
6mer
m5C RNA |
6LMS (A) |
1167 |
1.2 |
1.2 |
89.2 |
93.9 |
R |
||||
|
6GC5 (A:E) |
H.
sapiens
HuR RRM3 |
AU-rich
RNA |
6GD1 (A) |
1264 |
0.7 |
0.8 |
97.3 |
99.1 |
R |
||||
|
6HAU
(AB:D) |
Herpesvirus
saimiri mRNA export factor ICP27 homolog |
MRE
fragment of PAN RNA |
6HAT (AB) |
994 |
0.6 |
0.2 |
99.7 |
99.8 |
R |
||||
|
6I0V (A:B) |
D.
melanogaster DmTailor |
8-mer
RNA |
6I0S (A) |
1380 |
0.6 |
0.9 |
97.5 |
98.5 |
R |
||||
|
6L1W (A:C) |
M.
musculus
Zinc finger CCCH-type antiviral protein 1 |
CG
rich RNA |
3U9G (A) |
1356 |
1.6 |
2.0 |
84.8 |
91.5 |
S |
||||
|
6LLB (A:C) |
M.
psychrophilus MPY-RNase J |
6-mer
RNA |
5HAA (A) |
2527 |
0.8 |
0.7 |
97.8 |
99.0 |
R |
||||
|
6R9P (A:B) |
S.
cerevisiae apo Pan2 pseudoubiquitin hydrolase |
AAUUAA
RNA |
6R9I (A) |
974 |
0.8 |
0.6 |
95.6 |
97.4 |
R |
||||
|
6U9X (D:H) |
T.
brucei
MERS1 |
G rich
RNA |
6NL1 (A) |
2250 |
1.4 |
1.8 |
89.5 |
94.4 |
S |
||||
|
6L5N (A:C) |
H.
sapiens
DEAD-box RNA helicase DDX21 |
poly(U)-15mer |
6L5M (A) |
1201 |
1.4 |
1.2 |
92.1 |
95.9 |
R |
||||
|
6LT7
(AB:C) |
H.
sapiens
RPP20-RPP25 |
P3
domain of lncRNA RMRP |
6CWX (AB) |
5371 |
1.6 |
1.6 |
91.0 |
94.8 |
S |
||||
|
6U6Y
(AD:EH) |
H. sapiens
SAMHD1 |
ribo(CGCCU)-oligonucleotide |
5AO3 (AB) |
1996 |
0.5 |
0.3 |
99.2 |
99.7 |
R |
||||
|
6WXY
(BC:A) |
T.
succinifaciens card1 nuclease |
cA6-bound |
6WXW (AB) |
2186 |
0.5 |
0.6 |
99.4 |
99.8 |
R |
||||
|
6ZOT
(A:C) |
H.
sapiens
YTH domain-containing family protein 3 |
m6A
RNA |
8BS5 (A) |
|
1352 |
0.6 |
0.5 |
91.6 |
91.8 |
R |
|||
|
7C45 (A:D) |
T.
brucei
RNase D ribonuclease |
gRNA
U12 |
7C42 (A) |
2405 |
2.6 |
4.0 |
87.2 |
88.3 |
F |
||||
|
7DOL (A:C) |
M.
genitalium Ribonuclease R |
ssRNA |
7DCY (A) |
2076 |
1.0 |
0.9 |
81.0 |
85 |
R |
||||
|
7K5L(A:R) |
Ebola
virus Matrix protein VP40 |
HSP
RNA oligonucleotide |
4LDM (A) |
474 |
0.2 |
0.2 |
100.0 |
100.0 |
R |
||||
|
7EIU (A:C) |
S.
pombe
meiosis protein mei2 RRM3 |
8mer
meiRNA |
7EIO (A) |
2431 |
0.9 |
0.6 |
97.1 |
98.3 |
R |
||||
|
7KL3 (A:B) |
H1N1
california PA endonuclease |
RNA
oligomer AG*CAUC |
5CZN (A) |
848 |
0.2 |
0.3 |
98.9 |
98.9 |
R |
||||
|
7L6T (A:C) |
SARS-CoV-2
Nsp16/10 Heterodimer |
mRNA
capping |
7C2I (A) |
1120 |
0.6 |
1.0 |
98.7 |
99.4 |
R |
||||
|
7V4G (A:D) |
H.
sapiens
RNA demethylase ALKBH5 |
m6A-containing
ssRNA |
4O61 (A) |
1529 |
0.6 |
0.7 |
92.1 |
93.0 |
R |
||||
|
7VSJ (A:B) |
M.
Musculus
MmIMP3-RRM12 |
mRNA |
6FQ1 (A) |
830 |
0.5 |
0.5 |
96.8 |
97.5 |
R |
||||
|
7VKI (A:B) |
H
Sapiens
ESRP1 Qrrm2 |
mRNA |
2DHA (A) |
632 |
1.5 |
1.0 |
81.9 |
84.1 |
R |
||||
|
7VKL (A:B) |
M.
Musculus
MmIMP3-KH12 |
zipcode
RNA |
6GQE (A) |
1227 |
1.1 |
1.3 |
94.0 |
96.5 |
R |
||||
|
7Y7Q
(AB:CED) |
N.
Crasa QDE-1 |
synthetic
RNA |
2J7N (AB) |
3920 |
1.1 |
1.0 |
94.6 |
97.6 |
R |
||||
|
8DZK(A:F) |
E.
Histolytica Dbr1 |
bRNAs |
5K71 (A) |
1262 |
0.2 |
0.4 |
100.0 |
100.0 |
R |
||||
|
8EDJ (A:R) |
M.
mulatta
APOBEC3G |
RA3G-ssRNA-GA |
6P3X (A) |
1692 |
17.7 |
23.2 |
51.5 |
49.6 |
F |
||||
|
8AXF
(ABCD:Q) |
E.
Fici
nucleocapsid protein |
ssRNA |
8AX4
(ABCD) |
10949 |
3.7 |
3.2 |
87.6 |
86.9 |
F |
||||
|
8TG4 (A:C) |
A.
pernix Tpt1
|
2'-OH
RNA |
8TG3 (A) |
974 |
0.2 |
0.2 |
97.3 |
97.3 |
R |
||||
|
III. Bound-Unbound cases (10) |
|||||||||||||
|
(A) Complexes with tRNA (2) |
|||||||||||||
|
2ZM5 (A:C) |
E.
coli iso-pent-enyl-transferase |
tRNA-Phe |
3L0U (A) |
3936 |
4.2 |
6.5 |
|||||||
|
3ZJT (A:B) |
E.
coli
leucyl-tRNA synthetase |
tRNA-Leu |
2NQP* (F) |
4322 |
2.8 |
2.9 |
|||||||
|
(B) Ribosomal proteins (1) |
|||||||||||||
|
6AAX (A:B) |
H.
sapiens
Mitochondrial transcription factor B1 |
12s
rRNA |
6AAS (A) |
1758 |
3.9 |
6.1 |
|||||||
|
(C) Duplex RNA (5) |
|||||||||||||
|
1HQ1 (A:B) |
E.
coli
SRP |
4.5S
RNA domain IV |
1DUH (A) |
1364 |
38.3 |
30.0 |
|||||||
|
1JID (A:B) |
H.
sapiens
SRP19 |
SRP
RNA |
1D4R (A) |
1436 |
2.6 |
4.0 |
|||||||
|
2PJP (A:B) |
E.
coli
SelB |
SECIS
RNA |
1MFK (A) |
1300 |
2.5 |
3.6 |
|||||||
|
3BT7 (A:C) |
E.
coli
methyltransferase TrmA |
T-arm
analogue |
1EVV (A) |
2230 |
3.1 |
3.5 |
|||||||
|
6HTU
(ABC:DF) |
H.
sapiens
hStau1 dsRBD3-4 |
ARF1
RNA |
6HU6 (AE) |
3840 |
1.6 |
1.6 |
|||||||
|
(D) Single-stranded RNA (2) |
|||||||||||||
|
1LNG (A:B) |
M.
jannaschii SRP19 |
7S SRP
RNA |
1Z43 (A) |
2367 |
2.0 |
2.1 |
|||||||
|
2I82 (A:E) |
E.
coli
pseudouridine synthase RluA |
tRNA-Phe |
3L0U
(A:26-43) |
3018 |
4.2 |
4.7 |
|||||||
aFour-letter PDB code of the protein-RNA complexes with chain id of the protein and the RNA molecules in the
parenthesis.
The first model of each
NMR structures (shown in bold)
considered for 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).
bSurface area buried (BSA) between protein and RNA upon
complexation.
crmsd calculated considering the equivalent Cα
atoms.
drmsd calculated considering the equivalent phosphorus (P) atoms.
ermsd calculated considering the equivalent interface
atoms.
†Complexes for which only single chain is available in the unbound forms. The bound PDB chain used for superposition with unbound PDB chain
is underlined in bold font. (e.g. 2OZB AB:C)