Table 1.
New cases in the protein-protein docking Benchmark 4.0.
| Complex | Cat.a | PDB ID 1 | Protein 1 | PDB ID 2b | Protein 2 | RMSD (Å) | DASA (Å2)c |
|---|---|---|---|---|---|---|---|
| Rigid Body (33) | |||||||
| 1CLV_A:I | E | 1JAE_A | α-amylase | 1QFD_A(1) | α-amylase inhibitor | 0.86 | 2086 |
| 1FLE_E:I | E | 9EST_A | Elastase | 2REL_A(4) | Elafin | 1.02 | 1762 |
| 1GL1_A:I | E | 1K2I_1 | α-chymotrypsin | 1PMC_A(6) | Protease inhibitor LCMI II | 1.21 | 1590 |
| 1GXD_A:C | E | 1CK7_A | proMMP2 type IV collagenase | 1BR9_A | Metalloproteinase inhibitor 2 | 1.39 | 2445 |
| 1JTG_B:A | E | 3GMU_B | β-Lactamase inhibitory protein | 1ZG4_A | β-lactamase TEM-1 | 0.49 | 2599 |
| 1OC0_A:B | E | 1B3K_A | Plasminogen activator inhibitor-1 | 2JQ8_A(4) | Vitronectin Somatomedin B domain | 1 | 1312 |
| 1OYV_A:I | E | 1SCD_A | Subtilisin Carlsberg | 1PJU_A | Two-headed tomato inhibitor-II | 0.7 | 1929 |
| 1OYV_B:I | E | 1SCD_A | Subtilisin Carlsberg | 1PJU_A | Two-headed tomato inhibitor-II | 0.5 | 1279 |
| 2ABZ_B:E | E | 3I1U_A | Carboxypeptidase A1 | 1ZFI_A(1) | Leech carboxypeptidase inhibitor | 0.9 | 1443 |
| 2J0T_A:D | E | 966C_A | MMP1 Interstitial collagenase | 1D2B_A(20) | Metalloproteinase inhibitor 1 | 1.23 | 1476 |
| 2OUL_A:B | E | 3BPF_A | Falcipain 2 | 2NNR_A | Chagasin | 0.53 | 1932 |
| 3SGQ_E:I | E | 2QA9_E | Streptogrisin B | 2OVO_A | Ovomucoid inhibitor third domain | 0.39 | 1210 |
| 1FCC_AB:C | O | 1FC1_AB | Fc domain of IgG1 MO6 | 2IGG_A(3) | Strep. protein G C2 fragment | 0.93 | 1354 |
| 1FFW_A:B | O | 3CHY_A | Chemotaxis protein CheY | 1FWP_A | Chemotaxis protein CheA | 1.43 | 1166 |
| 1H9D_A:B | O | 1EAN_A | Runx1 domain of CBF α1 | 1ILF_A(1) | Dimerisation domain of CBF-β | 1.32 | 2121 |
| 1HCF_AB:X | O | 1B98_AM | Neurotrophin-4 | 1WWB_X | TrkB-d5 growth factors receptor | 0.88 | 2135 |
| 1JWH_CD:A | O | 3EED_AB | Casein kinase II β chain | 3C13_A | Casein kinase II α chain | 1.27 | 1451 |
| 1OFU_XY:A | O | 1OFT_AB | SulA (PA3008) | 2VAW_A | Cell division protein FtsZ | 1.1 | 1583 |
| 1PVH_A:B | O | 1BQU_A | IL6 receptor βchain D2-D3 domains | 1EMR_A | Leukemia inhibitory factor | 0.34 | 1403 |
| 1RV6_VW:X | O | 1FZV_AB | PIGF receptor binding domain | 1QSZ_A | Flt1 protein domain 2 | 1.09 | 1625 |
| 1US7_A:B | O | 2FXS_A | Heat shock protein 82 N-ter domain | 2W0G_A | HSP 90 co-chaperone CDC 37 C-ter domain | 1.06 | 1095 |
| 1WDW_BD:A | O | 1V8Z_AB | Tryptophan synthase β chain 1 | 1GEQ_A | Tryptophan synthase α chain | 1.29 | 3147 |
| 1XU1_ABD:T | O | 1U5Y_ABD | TNF domain of APRIL | 1XUT_A(11) | TNF receptor superfamily member 13B TACI CRD2 domain | 1.3 | 1696 |
| 1ZHH_A:B | O | 1JX6_A | Autoinducer 2-binding periplasmic protein LuxP | 2HJE_A | Autoinducer 2 sensor kinase/phosphatase LuxQ | 1.31 | 2189 |
| 2A5T_A:B | O | 1Y20_A | NMDA receptor R1-4A subunit ligand-binding core | 2A5S_A | NMDA receptor R2A subunit ligand-binding core | 1.28 | 1892 |
| 2A9K_A:B | O | 1U90_A | Ras-related protein Ral-A | 2C8B_X | Mono-ADP-ribosyltransferase C3 | 0.85 | 1750 |
| 2B4J_AB:C | O | 1BIZ_AB | Integrase (HIV-1) | 1Z9E_A(1) | PC4 and SFRS1 interacting protein | 0.99 | 1273 |
| 2FJU_B:A | O | 2ZKM_X | Phospholipase β 2 | 1MH1_A | Rac GTPase | 1.04 | 1245 |
| 2G77_A:B | O | 1FKM_A | GTPase-activating protein Gyp1 | 1Z06_A | Ras-related protein Rab-33B | 1.75 | 2524 |
| 2OOR_AB:C | O | 1L7E_AB | NAD(P) transhydrogenase subunit α part 1 | 1E3T_A | NAD(P) transhydrogenase subunit β | 1.42 | 2065 |
| 2VDB_A:B | O | 3CX9_A | Serum albumin | 2J5Y_A | Peptostreptococcal albumin-binding protein GA module | 0.47 | 1797 |
| 3BP8_AB:C | O | 1Z6R_AB | Mlc transcription regulator | 3BP3_A | PTS glucose-specific enzyme EIICB | 0.45 | 1390 |
| 3D5S_A:C | O | 1C3D_A | Complement C3d fragment | 2GOM_A | Fibrinogen-binding protein C-ter domain | 0.56 | 1620 |
| Medium Difficult (11) | |||||||
| 1JIW_P:I | E | 1AKL_A | Alkaline metalloproteinase | 2RN4_A(1) | Proteinase inhibitor | 2.07 | 1997 |
| 4CPA_A:I | E | 8CPA_A | Carboxypeptidase A | 1H20_A(9) | Potato carboxypeptidase inhibitor | 1.97 | 1175 |
| 1LFD_B:A | O | 5P21_A | Ras | 1LXD_A | RalGDS Ras-interacting domain | 1.79 | 1167 |
| 1MQ8_A:B | O | 1IAM_A | ICAM-1 domains 1-2 | 1MQ9_A | Integrin α-L I domain | 1.76 | 1252 |
| 1R6Q_A:C | O | 1R6C_X | Clp protease subunit ClpA | 2W9R_A | Clp protease adaptor protein ClpS | 1.67 | 1651 |
| 1SYX_A:B | O | 1QGV_A | Spliceosomal U5 15 kDa protein | 1L2Z_A(1) | CD2 receptor binding protein 2 C- ter fragment | 1.64 | 1292 |
| 2AYO_A:B | O | 2AYN_A | Ubiquitin carboxyl-terminal hydrolase 14 | 2FCN_A | Ubiquitin | 1.62 | 3026 |
| 2J7P_A:D | O | 1NG1_A | SRP GTPase Ffh | 2IYL_D | Cell division protein FtsY | 1.93 | 3008 |
| 2OZA_B:A | O | 3HEC_A | MAP kinase 14 | 3FYK_X | MAP kinase-activated protein kinase 2 | 1.89 | 6247 |
| 2Z0E_A:B | O | 2D1I_A | Cysteine protease Atg4B | 1V49_A(1) | Microtubule-associated proteins 1A/1B light chain 3B | 2.15 | 2477 |
| 3CPH_G:A | O | 3CPI_G | Ras-related protein Sec4 | 1G16_A | Rab GDP-dissociation inhibitor | 2.12 | 1684 |
| Difficult (8) | |||||||
| 1F6M_A:C | E | 1CL0_A | Thioredoxin reductase | 2TIR_A | Thioredoxin 1 | 4.9 | 1821 |
| 1ZLI_A:B | E | 1KWM_A | Carboxypeptidase B | 2JTO_A(6) | Tick carboxypeptidase inhibitor | 2.53 | 2083 |
| 2O3B_A:B | E | 1ZM8_A | NucA nuclease | 1J57_A | NuiA nuclease inhibitor | 3.13 | 1675 |
| 1JK9_B:A | O | 1QUP_A | CCS metallochaperone | 2JCW_A | SOD1 superoxide dismutase | 4.87 | 2130 |
| 1JZD_AB:C | O | 1JZO_AB | DsbC disulfide bond isomerase | 1JPE_A | DsbD disulfide bond isomerase | 2.71 | 2026 |
| 1ZM4_A:B | O | 1N0V_C | Elongation factor 2 | 1XK9_A | Diphtheria toxin A catalytic domain | 2.94 | 1554 |
| 2I9B_E:A | O | 1YWH_A | Urokinase plasminogen activator surface receptor | 2I9A_A | Urokinase-type plasminogen activator | 3.79 | 2370 |
| 2IDO_A:B | O | 1J54_A | DNA polymerase III ε exonuclease domain | 1SE7_A(1) | HOT protein (P1 phage) | 2.79 | 1953 |
a
Complex category labels: E = Enzyme/Inhibitor or Enzyme/Substrate, O = Other.
b
NMR model numbers from are shown in parenthesis.
c
Change in accessible surface area (ΔASA) upon complex formation, defined as the ASA of Protein 1 plus the ASA of Protein 2 minus the ASA of the Complex. ASA is calculated using NACCESS.