Computational Structural Biology Lab

Department of Biotechnology
Indian Institute of Technology Kharagpur

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.)

Table 1: The benchmark dataset of protein-RNA complexes.

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

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