Supplementary Information for Protein
RNA docking benchmark Version 2
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.
Click
here to download the protein-RNA docking benchmark dataset. (Description of
the dataset can be found here.)
Bounda |
Unbound (PDB id)a |
Bb |
rmsd |
fnat |
GDT_TS |
LGA_S |
Category |
|||||||
PDB id |
Protein |
RNA |
Protein |
RNA |
c-rmsdc |
p-rmsdd |
i-rmsde |
|||||||
Cα |
P |
Cα+P |
||||||||||||
I. Unbound-Unbound cases
(21) |
||||||||||||||
(A) Complexes with tRNA
(10) |
||||||||||||||
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 |
34.0 |
85.4 |
92.8 |
R |
1B23 (P:R) |
T. aquaticus EF-TU |
E. coli tRNA-Cys |
1TUI (A) |
1U0B* (A) |
2616 |
10.0 |
7.2 |
13.3 |
13.0 |
13.2 |
19.0 |
50.3 |
47.7 |
X |
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 |
70.8 |
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 |
41.3 |
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 |
46.2 |
77.1 |
68.4 |
R |
2DRB (A:B) |
A. fulgidus CCA-adding enzyme |
tRNAminiCCA |
1UET (A) |
3Q1Q* (C) |
3198 |
1.1 |
3.4 |
1.8 |
4.2 |
2.5 |
22.0 |
86.8 |
87.8 |
S |
2FMT (A:C) |
E. coli methionyl-tRNAfmet transformylase |
tRNAfmet |
1FMT (A) |
3CW6 (A) |
2940 |
1.2 |
2.3 |
0.9 |
2.5 |
1.7 |
44.8 |
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 |
20.0 |
6.4 |
12.9 |
43.6 |
74.5 |
73.9 |
X |
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 |
39.4 |
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 |
14.3 |
95.9 |
97.9 |
R |
(B)
Ribosomal proteins (3) |
||||||||||||||
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 |
14.3 |
73.4 |
70.4 |
X |
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 |
55.1 |
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 |
35.6 |
65.2 |
62.3 |
X |
(C)
Duplex RNA (4) |
||||||||||||||
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 |
50.0 |
64.1 |
62.7 |
X |
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 |
50.0 |
82.9 |
76.4 |
X |
2R8S (LH:R) |
M. musculus synthetic FAB |
ribozyme |
2HFF (AB) |
1HR2 (A) |
2510 |
1.6 |
4.3 |
2.9 |
2.1 |
2.5 |
50.9 |
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 |
31.3 |
44.2 |
40.2 |
X |
(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 |
62.1 |
97.0 |
98.9 |
R |
1WSU (A:E) |
M. thermoacetica elongation factor SelB |
SECIS
RNA |
1LVA (A) |
2RLU (A) |
940 |
0.7 |
4.2 |
0.5 |
1.1 |
0.8 |
73.7 |
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 |
72.7 |
49.6 |
49.8 |
R |
2BH2 (A:C) |
E. coli methyltransferase
RumA |
23S
rRNA |
1UWV (A) |
1JZX* (A:1915-1951) |
4491 |
1.4 |
9.8 |
0.7 |
10.5 |
6.0 |
30.4 |
86.0 |
93.5 |
R |
II. Unbound-Bound (95) |
||||||||||||||
(A) Complexes with tRNA
(16) |
||||||||||||||
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 |
X |
|||
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 |
X |
|||
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 |
X |
|||
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 |
|||
(B)
Ribosomal proteins (2) |
||||||||||||||
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 |
X |
|||
(C)
Duplex RNA (32) |
||||||||||||||
1MSW (D:R) |
Phage
T7 RNA polymerase |
RNA
transcript |
1ARO (P) |
1830 |
3.5 |
|
3.5 |
|
57.1 |
54.1 |
X |
|||
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) |
X. 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 |
X |
|||
2ZKO (AB:CD) |
NS1
protein of influenza A |
A-form
dsRNA |
2Z0A (AB) |
2466 |
0.6 |
|
0.8 |
|
97.7 |
98.8 |
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 |
X |
|||
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 |
|
22.0 |
|
45.6 |
43.1 |
X |
|||
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 |
|||
(D)
Single-stranded RNA (45) |
||||||||||||||
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 |
X |
|||
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 |
X |
|||
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 |
X |
|||
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 |
|
97.0 |
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 |
|
96.0 |
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 |
X |
|||
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 |
|||
5BUD (A:B) |
C. albicans decapping nuclease RAI1 |
polyU |
5BTH (A) |
1262 |
0.5 |
|
1.2 |
|
99.5 |
99.8 |
R |
|||
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 |
4ZLR (A) |
1639 |
0.4 |
|
0.6 |
|
99.8 |
99.9 |
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 |
|
|
|
||||
(C)
Duplex RNA (5) |
||||||||||||||
1HQ1 (A:B) |
E. coli SRP |
4.5S
RNA domain IV |
|
1DUH (A) |
1364 |
|
38.3 |
30.4 |
|
|
|
|||
1JID (A:B) |
H.
sapiens SRP19 |
SRP RNA |
|
1D4R (A) |
1436 |
|
2.6 |
4.0 |
|
|
|
|
||
2OZB (AB:C) |
H. sapiens ribonucleoprotein |
U4snRNA |
2XEB (AB) |
2569 |
|
11.0 |
12.5 |
|
|
|
||||
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 |
|
|
|
||||
(D)
Single-stranded RNA (3) |
||||||||||||||
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 |
|
|
|
||||
3IEV (A:D) |
A. aeolicus GTPase era |
16S rRNA |
1SDR (B) |
2273 |
|
7.6 |
8.4 |
|
|
|
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) the closet model
to the average structure of the ensemble was considered as the reference
structure 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
between protein and RNA upon complexation.
Crmsd calculated
considering the equivalent Cα atoms.
drmsd calculated
considering the equivalent P atoms.
ermsd
calculated considering the equivalent interface atoms.