Computational Structural Biology Lab
Source: http://www.csb.iitkgp.ac.in/applications/PRDBv3/Affinity.php Parent: http://www.csb.iitkgp.ac.in/
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PRDBv3_affinity
Table S2: The binding affinity benchmark dataset of protein-RNA complexes.
| Bounda | RNA length (nt) | Binding Affinity (Kd) (M)g | Temperature (K)h | pHi | *ΔG (kcal/mol)* j | Exp Techniquek | BSA (Å2)b | RMSD Å | Categoryf | PubMed ID(l) | ||||||
| PDB ID | Protein | RNA | Cα-rmsdc | P-rmsdd | i-rmsde | |||||||||||
| Crystal | Solution | Cα | P | |||||||||||||
| I. Unbound-Unbound cases (17) | ||||||||||||||||
| (A) Complexes with tRNA (7) | ||||||||||||||||
| 1ASY (A:R) | S. cerevisiae aspartyl-tRNA synthetase | tRNA-Asp | 75 | 76 | 3.0x10-8 | 310 | 5.5 | -10.66 | FBA | 4430 | 1.5 | 4.9 | 1.3 | 3.3 | R | 10452887 |
| 1QTQ (A:B) | E. coli glutaminyl-tRNA synthetase | tRNA-Gln | 75 | 76 | 3.6x10-7 | 310 | 5.2 | -9.13 | Binding kinetics | 5202 | 1.6 | 4.8 | 1.8 | 6.4 | S | 15845537 |
| 2DRB (A:B) | A. fulgidus CCA-adding enzyme | tRNAminiCCA | 35 | 73 | 6.7x10-8 | 298 | 8.5 | -9.78 | EMSA | 3198 | 1.1 | 3.4 | 1.8 | 4.2 | S | 14592988 |
| 2FMT (A:C) | E. coli methionyl-tRNAfmet transformylase | tRNAfmet | 77 | 77 | 1.36x10-7 | 310 | 7.6 | -9.73 | FBA | 2940 | 1.2 | 2.3 | 0.9 | 2.5 | R | 10089442 |
| 3HL2 (AA'BB':E) | H. sapiens selenium transferase | tRNA-Sec | 90 | 90 | 1.34x10-7 | 300 | 8.0 | -9.43 | MST | 2186 | 0.6 | 5.2 | 1.3 | 6 | R | 36929010 |
| 5X6B (IJEF:P) | M. jannaschii SepCysE-SepCysS | tRNA-Cys | 75 | 75 | 3.5x10-7 | 333 | 8.0 | -9.84 | ITC | 4240 | 0.6 | 3.2 | 1.2 | 6.4 | R | 29142195 |
| 6LVR (C:D) | A. thaliana PRORP1 | yeast tRNA-Phe | 76 | 76 | 3.9x10-7 | 298 | 7.8 | -8.74 | EMSA | 1055 | 3.4 | 1.3 | 4.4 | 1.1 | F | 36753552 |
| (B) Ribosomal proteins (3) | ||||||||||||||||
| 1DFU (P:MN) | E. coli ribosomal protein L25 | 5s rRNA | 19 | 120 | 6.7x10-8 | 298 | 7.6 | -9.78 | FBA | 1690 | 3 | 5.3 | 3 | 4.4 | F | 365228 |
| 1MMS (A:C) | T. maritimaribosomal protein L11 | 23S rRNA fragment | 58 | 60 | 1.20x10-7 | 298 | 7.5 | -9.44 | TSR | 2455 | 3.5 | 1.6 | 4.1 | 1.6 | F | 12954336 |
| 3IEV (A:D) | A. aeolicus GTPase era | 16S rRNA | 12 | 37 | 1.26x10-8 | 298 | 7.5 | -6.46 | ITC | 2273 | 0.5 | 7.6 | 0.5 | 8.4 | R | 21646538 |
| (C) Duplex RNA (5) | ||||||||||||||||
| 1OOA (A:C) | M. musculus NF-kappaB p50 | aptamer RNA | 29 | 29 | 5.4x10-9 | 298 | 7.5 | -11.27 | FBA | 1909 | 6.2 | 6.7 | 5.5 | 7 | F | 12886018 |
| 2R8S (LH:R) | M. musculus synthetic FAB | ribozyme | 159 | 159 | 5.1x10-8 | 298 | 7.5 | -9.94 | FBA | 2510 | 1.6 | 4.3 | 2.9 | 2.1 | S | 18162543 |
| 3SNP (A:C) | O. cuniculus iron regulatory protein 1 | ferritin H IRE RNA | 30 | 30 | 4.5x10-11 | 298 | 7.5 | -14.1 | FBA | 2872 | 0.7 | 3.8 | 14.5 | 3.3 | F | 17185597 |
| 2OZB (AB:C) | H. sapiens Ribonucleoprotein | U4snRNA | 33 | 32 | 8.0x10-6 | 277 | 8.0 | -6.46 | EMSA | 2569 | 1.9 | 11 | 1.9 | 13 | S | 21784869 |
| 7P0V (A:B) | H. sapiens SF3A1 ubiquitin-like domain | U1 snRNA SL-4 | 24 | 24 | 3.32x10-7 | 338 | 8.0 | -10.02 | SPR | 1210 | 1.5 | 1.1 | 1.7 | 0.9 | S | 35101980 |
| (D) Single-stranded RNA (2) | ||||||||||||||||
| 1JBS (A:C) | A. restrictus restrictocin | SRD RNA analogue | 29 | 29 | 1.0x10-6 | 298 | 7.2 | -8.18 | Fluorescence titration | 1310 | 0.7 | 3.4 | 0.6 | 3.2 | R | 11685244 |
| 1WSU (A:E) | M. thermoacetica elongation factor SelB | SECIS RNA | 23 | 23 | 1.0x10-6 | 277 | 5.4 | -7.6 | EMSA | 940 | 0.7 | 4.2 | 0.5 | 1.1 | R | 15665870 |
| II. Unbound-Bound (83) | ||||||||||||||||
| (A) Complexes with tRNA (5) | ||||||||||||||||
| 1U0B (B:A) | E. coli cysteinyl-tRNA synthetase | tRNA-Cys | 74 | 74 | 2.70x10-7 | 300 | 7.5 | -9.02 | Fluorescence titration | 4560 | 0.7 | 1.0 | R | 15489861 | ||
| 3ADB (A:C) | M. jannaschii O-phosphoseryl-tRNA kinase | tRNA-Sec | 92 | 92 | 4.8x10-8 | 338 | 7.5 | -11.31 | EMSA | 3099 | 22.4 | 27.3 | F | 20705242 | ||
| 4YVJ (AB:C) | H. influenzae tRNA methyltransferase D | tRNA | 74 | 74 | 2.80x10-7 | 300 | 8.0 | -9.0 | Fluorescence titration | 2313 | 0.7 | 1.3 | R | 26183229 | ||
| 5B63 (A:B) | E.coli arginyl-tRNA synthetase | tRNA-Arg | 77 | 77 | 2.20x10-7 | 294 | 7.4 | -8.96 | Fluorescence titration | 3360 | 1.2 | 1.5 | S | 29678554 | ||
| 7E8O (AB:X) | P. bacterium PRORP | pre-tRNA-His | 85 | 85 | 4.30x10-6 | 277 | 8.0 | -6.8 | EMSA | 801 | 1.8 | 1 | R | 35484139 | ||
| (B) Ribosomal proteins (2) | ||||||||||||||||
| 1SDS (C:FF') | M. jannaschii 50S ribosomal protein L7Ae | box H/ACA sRNA | 15 | 84 | 7.5x10-8 | 277 | 7.4 | -9.03 | EMSA | 1200 | 0.3 | 0.4 | R | 12560482 | ||
| 5WTY (A:C) | S. cerevisiae nucleolar protein 9 | 18s rRNA | 18 | 18 | 2.0x10-7 | 300 | 7.9 | -9.2 | EMSA | 3205 | 2.5 | 2.6 | S | 28053123 | ||
| (C) Duplex RNA (26) | ||||||||||||||||
| 1YVP (B:EFH) | X. laevis Ro autoantigen | Y RNA | 10 | 97 | 5.2x10-9 | 277 | 7.5 | -10.49 | EMSA | 4207 | 1.4 | 1.3 | R | 15907467 | ||
| 2AZ0 (AB:CD) | Flock house virus B2 | siRNA | 18 | 19 | 1.4x10-9 | 277 | 7.5 | -11.22 | EMSA | 2264 | 1.3 | 1 | R | 16228003 | ||
| 2QUX (AB:C) | Pseudomonas phage PP7 coat protein | hairpin RNA | 25 | 27 | 1.26x10-9 | 295 | 7.5 | -12.01 | EMSA | 1754 | 0.9 | 0.5 | R | 18066080 | ||
| 2Y8W (A:B) | T. thermophilus endoribonuclease Cse3 | hairpin RNA | 20 | 20 | 3.6x10-9 | 338 | 7.5 | -13.05 | EMSA | 3258 | 1.1 | 3.1 | F | 21572442 | ||
| 2ZKO (AB:CD) | NS1 protein of influenza A | A-form dsRNA | 21 | 21 | 1.2x10-6 | 298 | 7.4 | -8.07 | ITC | 2466 | 0.6 | 0.8 | R | 18813227 | ||
| 3A6P (AC:DE) | H. sapiens exp-5: Ran GTP | pre-microRNA | 24 | 30 | 6.5x10-9 | 300 | 7.6 | -9.87 | EMSA | 4223 | 1.2 | 1.4 | R | 21947008 | ||
| 3DD2 (H:B) | H. sapiens thrombin | 26-mer RNA | 26 | 40 | 5.4x10-10 | 310 | 7.4 | -13.14 | FBA | 1822 | 0.6 | 0.5 | R | 11735341 | ||
| 3EQT (AB:CD) | H. sapiens helicase DHX58 | dsRNA | 8 | 20 | 1.05x10-7 | 298 | 8.0 | -9.51 | Fluorescence titration | 2705 | 1.2 | 1.2 | R | 19278996 | ||
| 3KS8 (AB:EF) | R. ebolavirus polymerase cofactor VP35 | dsRNA | 18 | 18 | 8.9x10-7 | 300 | 7.5 | -8.31 | Dot blot | 1663 | 0.6 | 0.4 | R | 20018665 | ||
| 3MOJ (B:A) | B. subtilis helicase dbpA | E.coli 23S rRNA fragment | 74 | 74 | 5.4x10-11 | 273 | 7.5 | -12.82 | EMSA | 1758 | 1.0 | 1.0 | R | 20673833 | ||
| 3O3I (X:A) | H. sapiens Hiwi1 PAZ domain | piRNA | 14 | 14 | 1.66x10-5 | 298 | 8.0 | -6.52 | ITC | 923 | 2.1 | 2.7 | S | 21193640 | ||
| 3RW6 (A:H) | H. sapiens nuclear RNA export factor 1 | CTE RNA | 62 | 62 | 9.0x10-8 | 298 | 7.5 | -9.6 | ITC | 2699 | 13.5 | 19 | F | 21822283 | ||
| 4ERD (AB:CD) | T. thermophila p65 C-terminal domain | stem IV of telomerase RNA | 22 | 22 | 1.01x10-7 | 298 | 7.0 | -9.53 | ITC | 3280 | 1.5 | 1.2 | R | 22705372 | ||
| 4ZT0 (A:B) | S. pyogenes CRISPR-associated endonuclease Cas9 | single-guide RNA | 85 | 20 | 6.8x10-10 | 300 | 7.5 | -12.58 | FBA | 10845 | 29.6 | 22 | F | 26113724 | ||
| 5F5H (A:C) | M. musculus Roquin-1 | Ox40 3'-UTR | 22 | 22 | 8.10x10-8 | 283 | 7.4 | -9.18 | SPR | 1618 | 0.5 | 0.6 | R | 27010430 | ||
| 5WTK (A:B) | L. shahii CRISPR-associated endoribonuclease C2c2 | crRNA | 58 | 170 | 4.60x10-8 | 277 | 7.5 | -9.3 | EMSA | 8811 | 4.9 | 4.0 | F | 27256883 | ||
| 5ZQ8 (A:D) | S. pneumoniae RlmCD | 23S rRNA U747 stemloop | 12 | 12 | 5.0x10-7 | 310 | 8.0 | -8.94 | EMSA | 1992 | 1.5 | 1.2 | R | 30388185 | ||
| 6D12 (B:C) | H. sapiens xRRM domain of human Larp7 | 7SK stem-loop 4 RNA | 38 | 25 | 1.29x10-7 | 295 | 7.0 | -9.30 | ITC | 1428 | 2.1 | 1.6 | S | 29946027 | ||
| 6DCB (A:B) | H. sapiens methylphosphate capping enzyme | 5' end of 7SK RNA | 36 | 36 | 1.0x10-7 | 298 | 7.5 | -9.55 | ITC | 697 | 0.7 | 0.3 | R | 30559425 | ||
| 6FQ3 (A:B) | D. rerio E3 ubiquitin-protein ligase TRIM71 | lin-29A 5'UTR | 13 | 13 | 1.57x10-6 | 300 | 8.0 | -7.78 | FP | 986 | 7.9 | 2 | S | 29674686 | ||
| 6SY4 (AB:C) | E. coli TetR | TetR-binding aptamer K1 | 43 | 43 | 5.60x10-9 | 298 | 7.4 | -11.25 | ITC | 1702 | 1.7 | 2 | S | 32052019 | ||
| 6PZQ (AB:IJ) | HRSV matrix M2-1 | Gene-End RNA | 7 | 7 | 8.67x10-7 | 300 | 7.4 | -8.32 | MST | 668 | 0.9 | 0.5 | R | 32697936 | ||
| 6ZDP (A:B) | C. tropicalis telomerase reverse transcriptase (724) | TWJ fragment of telomeric RNA | 72 | 72 | 2.70x10-8 | 293 | 7.8 | -10.15 | ITC | 2629 | 4.1 | 8.4 | F | 33856462 | ||
| 7KKV (A:B) | A. halodurans OapB protein | OLE RNA target | 60 | 100 | 7.0x10-10 | 277 | 7.5 | -11.6 | EMSA | 1365 | 0.7 | 0.7 | R | 32376692 | ||
| 7OG0 (A:EE') | H. influenzae SapA | dsRNA | 17 | 17 | 4.4x10-6 | 298 | 8.0 | -7.3 | ITC | 597 | 3 | 2.1 | S | 34653190 | ||
| 7ZLQ (A:DE) | H. Sapiens ADAR1-dsRBD3 | dsRNA | 13 | 24 | 1.25x10-7 | 298 | 7.0 | -9.41 | ITC | 784 | 1.3 | 0.6 | R | BioRxiv | ||
| (D) Single-stranded RNA (50) | ||||||||||||||||
| 1C9S (L:W1-7) | G. stearothermophilus TRAP | ssRNA | 55 | 55 | 5.0x10-10 | 328 | 8.0 | -13.96 | FBA | 1027 | 0.3 | 0.2 | R | 10499579 | ||
| 1CVJ (A:M) | H. sapiens poly(A)-binding protein | polyA | 11 | 25 | 6.70x10-10 | 277 | 7.4 | -11.63 | EMSA | 2822 | 2.7 | 3.9 | F | 14717712 | ||
| 1K8W (A:B) | E. coli pseudouridine synthase B | T stem-loop RNA | 22 | 22 | 7.0x10-7 | 300 | 7.5 | -8.45 | Fluorescence titration | 2973 | 1.9 | 1.3 | R | 24371284 | ||
| 1KQ2 (ABHIKM:R) | S. aureus Hfq | 7-mer RNA | 7 | 7 | 5.6x10-8 | 298 | 7.5 | -9.88 | Fluorescence titration | 3026 | 0.6 | 0.5 | R | 12093755 | ||
| 1M8W (A:CE) | H. sapiens pumilio-homology domain | Nre1-19 RNA | 16 | 34 | 6.0x10-11 | 300 | 7.4 | -14.03 | EMSA | 2110 | 0.8 | 0.7 | R | 12202039 | ||
| 1WPU (A:C) | B. subtilis HutP antitermination protein | hut mRNA | 7 | 21 | 5.40x10-8 | 300 | 7.5 | -9.98 | FBA | 1360 | 0.2 | 0.2 | R | 15758992 | ||
| 2A8V (B:E) | E. coli RHO | Cytosine rich RNA | 6.0 | 10 | 5.0x10-6 | 298 | 8.0 | -7.22 | FBA | 720 | 1 | 1.6 | S | 8632473 | ||
| 2ASB (A:B) | M. tuberculosis Nus A antiterminator | BoxC rRNA | 11 | 13 | 1.15x10-7 | 291 | 7.8 | -9.23 | ITC | 2320 | 1.1 | 0.8 | R | 16193062 | ||
| 2IX1 (A:B) | E. coli RNase II | polyA | 13 | 25 | 5.3x10-9 | 277 | 8.0 | -10.48 | SPR | 4160 | 1.6 | 0.9 | R | 18337246 | ||
| 2JEA (AB:C) | S. solfataricus exosome | substrate RNA | 35 | 7.0 | 1.1x10-6 | 293 | 7.5 | -7.98 | ITC | 1533 | 0.3 | 0.3 | R | 17159918 | ||
| 2XGJ (A:C) | S. cerevisiae Mtr4 | polyA | 5 | 21 | 2.80x10-6 | 303 | 6.5 | -7.7 | Fluorescence titration | 1389 | 4.1 | 3.1 | F | 25414331 | ||
| 2XNR (A:C) | S. cerevisiae Nab3-RRM | UCUU recognition sequence | 12 | 12 | 1.1x10-4 | 298 | 7.3 | -5.39 | Fluorescence titration | 926 | 1.0 | 1.2 | R | 20805243 | ||
| 2XZO (A:D) | H. sapiens Upf1 helicase | polyU | 7 | 15 | 2.02x10-7 | 293 | 7.5 | -8.97 | Fluorescence titration | 2006 | 6.2 | 5.0 | F | 21419344 | ||
| 3AEV (B:C) | P. horikoshii Dim2p | P. horikoshii 16S rRNA fragment | 11 | 11 | 9.8x10-10 | 298 | 8.5 | -12.28 | SPR | 2416 | 0.7 | 0.5 | R | 20363226 | ||
| 3BX2 (A:C) | S. cerevisiae PUF4 | 3' UTR binding sequence | 9 | 9 | 1.36x10-8 | 277 | 7.5 | -9.96 | EMSA | 2467 | 0.6 | 0.5 | R | 18327269 | ||
| 3D2S (A:E) | H. sapiens MBNL1 ZnF3/4 | pre-mRNA | 6 | 18 | 4.0x10-8 | 293 | 7.2 | -9.91 | Fluorescence titration | 569 | 0.8 | 0.6 | R | 19043415 | ||
| 3MDG (AB:C) | H. sapiens CFI(m)25 | pre-mRNA | 6 | 21 | 6.45x10-7 | 303 | 8.0 | -8.58 | EMSA | 1069 | 0.5 | 0.9 | R | 20479262 | ||
| 3NMR (A:B) | H. sapiens CUG-binding protein 1 | UGU-rich mRNA | 12 | 12 | 6.5x10-7 | 298 | 7.0 | -8.43 | ITC | 1096 | 2.7 | 2.2 | S | 20947024 | ||
| 3O8C (A:C) | HCV NS3 helicase | polyU | 6 | 18 | 8.7x10-7 | 298 | 7.5 | -8.26 | EMSA | 1909 | 1 | 1.1 | R | 12162749 | ||
| 3PF4 (B:R) | B. subtilis CspB | ssRNA | 7 | 7 | 1.59x10-7 | 288 | 7.0 | -8.95 | Fluorescence titration | 963 | 0.5 | 0.4 | R | 22128343 | ||
| 4H5P (AB:E) | Rift valley fever virus nucleocapsid | polyU | 14 | 25 | 9.6x10-8 | 298 | 7.8 | -9.56 | Fluorescence titration | 4482 | 0.9 | 2.1 | S | 23129612 | ||
| 4M59 (AB:CD) | Z. mays chloroplast ppr10 | psaJ RNA | 18 | 18 | 1.02x10-7 | 295 | 7.5 | -9.44 | EMSA | 7842 | 10.5 | 7.1 | F | 24162847 | ||
| 4MDX (AB:C) | B. subtilis mRNA interferase MazF | mRNA | 9 | 9 | 6.40x10-8 | 293 | 8.0 | -9.64 | ITC | 2127 | 0.7 | 1.6 | S | 24120662 | ||
| 5DET (AB:PQ) | H. sapiens RBPMS | CAC containing ssRNA | 5 | 17 | 9.0x10-7 | 293 | 7.5 | -8.11 | ITC | 2137 | 1.2 | 1.6 | S | 26347403 | ||
| 5EIM (A:C) | S. pombe YTH domain of spMmi1 | synthetic RNA | 8 | 8 | 1.10x10-6 | 298 | 7.5 | -8.12 | ITC | 1529 | 0.6 | 1.3 | R | 28735863 | ||
| 5ELS (AC:HI) | H. sapiens KH domain of T-STAR | synthetic RNA | 6 | 5 | 3.70x10-5 | 300 | 7.0 | -6.08 | FP | 2313 | 1.5 | 2.9 | S | 26758068 | ||
| 5EX7 (A:B) | D. melanogaster Brat NHL domain | hunchback mRNA | 8 | 100 | 1.37x10-7 | 293 | 8.0 | -9.2 | MST | 1639 | 0.4 | 0.6 | R | 24696456 | ||
| 5GXH (A:B) | H. sapiens Gemin5 | Pre-snRNAs | 8 | 8 | 2.40x10-6 | 298 | 7.5 | -7.66 | ITC | 1711 | 0.4 | 0.2 | R | 27881600 | ||
| 5LTA (A:E) | T. thermophila DEAH-box heicase Prp43 | Synthetic RNA | 16 | 16 | 4.98x10-6 | 298 | 7.5 | -7.23 | Fluorescence titration | 2287 | 2.4 | 2.2 | S | 28092261 | ||
| 5SZE (A:C) | A. aeolicus Hfq-RNA | PolyU | 6 | 6 | 2.13x10-8 | 298 | 8.0 | -10.46 | FP | 502 | 1.1 | 0.5 | R | 28375142 | ||
| 5V7C (B:C) | H. sapiens LARP1-unique domain DM15 | 5'TOP motif | 8 | 42 | 7.50x10-6 | 298 | 7.5 | -6.99 | EMSA | 1238 | 0.4 | 0.5 | R | 28379136 | ||
| 5WWX (A:C) | H. sapiens KH2 domain of MEX-3C | 5-mer RNA | 5 | 6 | 3.15x10-6 | 293 | 7.5 | -7.38 | ITC | 1380 | 0.8 | 0.9 | R | 28808060 | ||
| 5ZSC (A:C) | M. mulatta toll-like receptor 7 | CCUUCA RNA | 6 | 6 | 1.0x10-7 | 298 | 5.5 | -9.55 | ITC | 1227 | 0.5 | 0.5 | R | 30566863 | ||
| 6A6J (A:B) | D. rerio cold shock domain of Ybx1 | 6mer m5C RNA | 6 | 6 | 2.23x10-7 | 298 | 8.0 | -9.07 | ITC | 1167 | 1.2 | 1.2 | R | 31399345 | ||
| 6GC5 (A:E) | H. sapiens HuR RRM3 | AU-rich RNA | 11 | 11 | 6.50x10-7 | 298 | 7.0 | -8.44 | ITC | 1264 | 0.7 | 0.8 | R | 30718402 | ||
| 6L1W (A:C) | M. musculus Zinc finger CCCH-type antiviral protein 1 | CG rich RNA | 7 | 7 | 1.20x10-7 | 298 | 7.5 | -9.44 | ITC | 1356 | 1.6 | 2 | S | 31914396 | ||
| 6LLB (A:C) | M. psychrophilus MPY-RNase J | 6-mer RNA | 6 | 5 | 4.0x10-7 | 277 | 7.5 | -8.11 | EMSA | 2527 | 0.8 | 0.7 | R | 28795788 | ||
| 6U9X (D:H) | T. brucei MERS1 | G rich RNA | 11 | 11 | 3.90x10-8 | 298 | 7.5 | -10.1 | FP | 2250 | 1.4 | 1.8 | S | 31704716 | ||
| 6L5N (A:C) | H. sapiens DEAD-box RNA helicase DDX21 | poly(U)-15mer | 15 | 15 | 2.90x10-5 | 300 | 7.5 | -6.23 | MST | 1201 | 1.4 | 1.2 | R | 32714761 | ||
| 6LT7 (AB:C) | H. sapiens RPP20-RPP25 | P3 domain of lncRNA RMRP | 50 | 50 | 7.69x10-8 | 295 | 7.5 | -9.6 | EMSA | 5371 | 1.6 | 1.6 | S | 20215441 | ||
| 6U6Y (AD:EH) | H. sapiens SAMHD1 | ribo(CGCCU)-oligonucleotide | 5 | 5 | 1.10x10-7 | 300 | 8.0 | -9.55 | Fluorescence titration | 1996 | 0.5 | 0.3 | R | 33531504 | ||
| 6WXY (BC:A) | T. succinifaciens card1 nuclease | cA6-bound | 6 | 6 | 7.80x10-8 | 293 | 7.5 | -9.53 | ITC | 2186 | 0.5 | 0.6 | R | 33461211 | ||
| 7C45 (A:D) | T. brucei RNase D ribonuclease | gRNA U12 | 12 | 12 | 1.0x10-6 | 277 | 8.0 | -7.6 | EMSA | 2405 | 2.6 | 4.0 | F | 33332555 | ||
| 7DOL (A:C) | M. genitalium Ribonuclease R | ssRNA | 6 | 24 | 6.62x10-9 | 298 | 6.8 | -11.15 | FP | 2076 | 1.0 | 0.9 | R | 33788943 | ||
| 7EIU (A:C) | S. pombe meiosis protein mei2 RRM3 | 8mer meiRNA | 6 | 8 | 5.30x10-7 | 293 | 6.5 | -8.41 | FP | 2431 | 0.9 | 0.6 | R | 35512546 | ||
| 7L6T (A:C) | SARS-CoV-2 Nsp16/10 Heterodimer | mRNA capping | 7 | 7 | 2.80x10-5 | 298 | 8.0 | -6.21 | ITC | 1120 | 0.6 | 1.0 | R | 34131072 | ||
| 7V4G (A:D) | H. sapiens RNA demethylase ALKBH5 | m6A-containing ssRNA | 8 | 11 | 5.29x10-5 | 298 | 7.5 | -5.83 | MST | 1529 | 0.6 | 0.7 | R | 27156733 | ||
| 7VKI (A:B) | H Sapiens ESRP1 Qrrm2 | mRNA | 12 | 6 | 6.75x10-7 | 298 | 8.0 | -8.41 | ITC | 632 | 1.5 | 1 | R | 38015468 | ||
| 8EDJ (A:R) | M. mulatta APOBEC3G | RA3G-ssRNA-GA | 10 | 10 | 4.70x10-8 | 277 | 7.5 | -9.29 | EMSA | 1692 | 17.7 | 23.2 | F | 36470880 | ||
| 8AXF (ABCD:Q) | E. Fici nucleocapsid protein | ssRNA | 42 | 42 | 1.76x10-7 | 298 | 7.4 | -9.21 | ITC | 10949 | 3.7 | 3.2 | F | 37039649 | ||
| III. Bound-Unbound cases (5) | ||||||||||||||||
| (B) Ribosomal proteins (1) | ||||||||||||||||
| 6AAX (A:B) | H. sapiens Mitochondrial transcription factor B1 | 12s rRNA | 28 | 28 | 4.0x10-7 | 310 | 8.0 | -9.08 | EMSA | 1758 | 3.9 | 6.1 | 31251801 | |||
| (C) Duplex RNA (4) | ||||||||||||||||
| 1HQ1 (A:B) | E. coli SRP | 4.5S RNA domain IV | 49 | 49 | 3.33x10-11 | 300 | 7.5 | -14.38 | FBA | 1364 | 38.3 | 30 | 11243816 | |||
| 2PJP (A:B) | E. coli SelB | SECIS RNA | 23 | 23 | 3.0x10-10 | 298 | 6.0 | -12.98 | EMSA | 1300 | 2.5 | 3.6 | 17537456 | |||
| 3BT7 (A:C) | E. coli methyltransferase TrmA | T-arm analogue | 19 | 19 | 2.0x10-8 | 300 | 7.5 | -10.57 | FBA | 2230 | 3.1 | 3.5 | 32597953 | |||
| 6HTU (ABC:DF) | H. sapiens hStau1 dsRBD3-4 | ARF1 RNA | 19 | 19 | 1.40x10-8 | 277 | 9.7 | -9.95 | EMSA | 3840 | 1.6 | 1.6 | 30456389 |
aFour-letter PDB code of the protein-RNA complexes with the chain ID(s) of the protein and the RNA molecules in the parentheses. Symmetry-related chains are primed (e.g., FF' in1SDS).
bSurface area buried 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.
fClassification of different categories: Rigid [R], Semi-flexible [S] Full-flexible [F].
gBinding affinity values taken from literature.
hAbsolute temperature at which affinity is measured.
ipH at which affinity is measured.
jGibbs free energy of association calculated from ΔG = RTlnKd , where R is the gas constant and T is the absolute temperature.
kExperimental methods used for the determination of Kd :
Filtration assay or Filter binding assay (FBA), Fluorescence titration (FT), Electrophoretic mobility shift assay (EMSA), Binding kinetics (KB), Isothermal titration calorimetry (ITC),\ Surface plasma resonance (SPR), Fluorescence polarization (FP), Microscale thermophoresis (MST), TSR Methyltransferase Assay (TSR) and Dot Blot RNA-Binding Assays (Dot blot).
lPubMed accession ID of literature.
†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)