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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 | |||||||
| 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. coliaspartyl-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 methyltransferaseRlmN | 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. stearothermophilusTRAP | 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.