Supplementary
Information for |
|
|
|
|
|
|
|
|
|
|
|
Hwang,
H, Vreven, T, Janin, J and Weng, Z., Protein-Protein Docking Benchmark Version 4.0.,
Proteins., 2010 Nov 15;78(15):3111-4. |
|
|
|
Download cleaned-up PDB files for the benchmark in a
gzipped archive |
Download TableS1 in excel file |
|
|
|
|
|
|
|
|
|
|
|
|
Updates and corrections (August,16,2010): |
Please note that 1AY7 protein 1 1RGH is corrected from Barnase to RNase Sa. |
|
Updates and corrections (March,9,2011): |
1TFH contains two chains, A and B, for the same protein with an identical sequence. The two chains have different missing residues. |
1TFH chain A is used as a unbound constituent of 1AHW and 1TFH chain B is used as as unbound constituent of 1JPS and 1FAK. |
To make them consistent, we added 1JPS_l_u.pdb.2 and 1FAK_l_u.pdb.2 using 1TFH chain A for the downloadable files. |
|
Updates and corrections (July,6,2012): |
Complex 1BKD Protein 2 2II0 chain B was corrected to chain A (It was a typo in the table). |
iRMSD of the following 6 cases were corrected and, therefore, docking difficult classes were changed for some of them. |
1JK9: iRMSD corrected from 4.87 to 2.51, no change in docking difficulty. |
1ZM4: iRMSD corrected from 2.94 to 2.11, docking difficulty corrected from Difficult to Medium. |
2AYO: iRMSD corrected from 1.62 to 1.39, docking difficulty corrected from Medium to Rigid. |
2G77: iRMSD corrected from 1.75 to 1.08, no change in docking difficult. |
4CPA: iRMSD corrected from 1.97 to 0.62, docking difficulty corrected from Medium to Rigid. |
BOYV(1OYV_B:I): iRMSD corrected from 0.5 to 0.47, no change in docking difficult. |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Follow
the "info" link in the leftmost column to view bound/unbound chain
BLAST alignments and |
|
|
|
potentially
useful comments about individual benchmark cases |
|
|
|
|
|
|
|
|
|
|
|
Table SI. Protein-Protein Docking Benchmark 4.0 |
|
|
|
|
|
|
|
+Info |
Complex |
Cat.a |
PDBid 1 |
Protein 1 |
HETATMs |
PDBid 2 |
Protein 2 |
HETATMs |
RMSDb(Å) |
DASAc(Å2) |
Multimer |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Rigid-body
(123) |
|
|
|
|
|
|
|
|
|
|
info |
1AHW_AB:C |
A |
1FGN_LH |
Fab 5g9 |
|
1TFH_A |
Tissue factor |
|
0.69 |
1899 |
|
|
info |
1BVK_DE:F |
A |
1BVL_BA |
Fv Hulys11 |
|
3LZT_ |
HEW lysozyme |
|
1.24 |
1321 |
|
|
info |
1DQJ_AB:C |
A |
1DQQ_CD |
Fab Hyhel63 |
|
3LZT_ |
HEW lysozyme |
|
0.75 |
1765 |
|
|
info |
1E6J_HL:P |
A |
1E6O_HL |
Fab |
|
1A43_ |
HIV-1 capsid protein p24 |
|
1.05 |
1245 |
|
|
info |
1JPS_HL:T |
A |
1JPT_HL |
Fab D3H44 |
|
1TFH_B |
Tissue factor |
|
0.51 |
1852 |
|
|
info |
1MLC_AB:E |
A |
1MLB_AB |
Fab44.1 |
|
3LZT_ |
HEW lysozyme |
|
0.6 |
1392 |
|
|
info |
1VFB_AB:C |
A |
1VFA_AB |
Fv D1.3 |
|
8LYZ_ |
HEW lysozyme |
|
1.02 |
1383 |
|
|
info |
1WEJ_HL:F |
A |
1QBL_HL |
Fab E8 |
|
1HRC_ |
Cytochrome C |
HEM,ACE |
0.31 |
1177 |
|
|
info |
2FD6_HL:U |
A |
2FAT_HL |
Plasminogen receptor antibody |
|
1YWH_A |
Plasminogen activator receptor |
|
1.07 |
1139 |
|
|
info |
2I25_N:L |
A |
2I24_N |
Shark single domain antigen receptor |
|
3LZT |
Lysozyme |
|
1.21 |
1425 |
|
|
info |
2VIS_AB:C |
A |
1GIG_LH |
Fab |
|
2VIU_ACE |
Flu virus hemagglutinin |
|
0.8 |
1296 |
Ligand Trimer Created |
|
info |
1BJ1_HL:VW |
AB |
1BJ1_HL |
Fab |
|
2VPF_GH |
vEGF |
|
0.5 |
1731 |
|
|
info |
1FSK_BC:A |
AB |
1FSK_BC |
Fab |
|
1BV1_ |
Birch pollen antigen Bet V1 |
|
0.45 |
1623 |
|
|
info |
1I9R_HL:ABC |
AB |
1I9R_HL |
Fab |
|
1ALY_ABC |
Cd40 ligand |
|
1.3 |
1498 |
Receptor Trimer Created |
|
info |
1IQD_AB:C |
AB |
1IQD_AB |
Fab |
|
1D7P_M |
Factor VIII domain C2 |
|
0.48 |
1976 |
|
|
info |
1K4C_AB:C |
AB |
1K4C_AB |
Fab |
|
1JVM_ABCD |
Potassium Channel Kcsa |
|
0.53 |
1601 |
Ligand Tetramer Created |
|
info |
1KXQ_H:A |
AB |
1KXQ_H |
Camel VHH |
|
1PPI_ |
Pancreatic alpha-amylase |
|
0.72 |
2172 |
|
|
info |
1NCA_HL:N |
AB |
1NCA_HL |
Fab |
|
7NN9_ |
Flu virus neuraminidase N9 |
|
0.24 |
1953 |
|
|
info |
1NSN_HL:S |
AB |
1NSN_HL |
Fab N10 |
|
1KDC_ |
Staphylococcal nuclease |
|
0.35 |
1776 |
|
|
info |
1QFW_HL:AB |
AB |
1QFW_HL |
Fv |
|
1HRP_AB |
Human chorionic gonadotropin |
|
1.31 |
1580 |
|
|
info |
1QFW_IM:AB |
AB |
1QFW_IM |
Fv |
|
1HRP_AB |
Human chorionic gonadotropin |
|
0.73 |
1637 |
|
|
info |
2JEL_HL:P |
AB |
2JEL_HL |
Fab Jel42 |
|
1POH_ |
HPr |
|
0.17 |
1501 |
|
|
info |
1AVX_A:B |
E |
1QQU_A |
Porcine trypsin |
|
1BA7_B |
Soybean trypsin inhibitor |
|
0.47 |
1585 |
|
|
info |
1AY7_A:B |
E |
1RGH_B |
RNase Sa |
|
1A19_B |
Barstar |
|
0.54 |
1237 |
|
|
info |
1BVN_P:T |
E |
1PIG_ |
a-amylase |
|
1HOE_ |
Tendamistat |
|
0.87 |
2222 |
|
|
info |
1CGI_E:I |
E |
2CGA_B |
Bovine chymotrypsinogen |
|
1HPT_ |
PSTI |
|
2.02 |
2053 |
|
|
info |
1CLV_A:I |
E |
1JAE_A |
a-amylase |
|
1QFD_A(1) |
a-amylase inhibitor |
|
0.86 |
2087 |
|
|
info |
1D6R_A:I |
E |
2TGT_ |
Bovine trypsin |
|
1K9B_A |
Bowman-Birk inhibitor |
|
1.14 |
1408 |
|
|
info |
1DFJ_E:I |
E |
9RSA_B |
Ribonuclease A |
|
2BNH_ |
Rnase inhibitor |
ACE |
1.02 |
2582 |
|
|
info |
1E6E_A:B |
E |
1E1N_A |
Adrenoxin reductase |
FAD |
1CJE_D |
Adrenoxin |
|
1.33 |
2315 |
|
|
info |
1EAW_A:B |
E |
1EAX_A |
Matriptase |
|
9PTI_ |
BPTI |
|
0.54 |
1866 |
|
|
info |
1EWY_A:C |
E |
1GJR_A |
Ferredoxin reductase |
FAD |
1CZP_A |
Ferredoxin |
|
0.8 |
1502 |
|
|
info |
1EZU_C:AB * |
E |
1TRM_A |
D102N Trypsin |
|
1ECZ_AB |
Ecotin |
|
1.21 |
2751 |
|
|
info |
1F34_A:B |
E |
4PEP_ |
Porcine pepsin |
|
1F32_A |
Ascaris inhibitor 3 |
|
0.93 |
3038 |
|
|
info |
1FLE_E:I |
E |
9EST_A |
Elastase |
|
2REL_A(4) |
Elafin |
|
1.02 |
1763 |
|
|
info |
1GL1_A:I |
E |
1K2I_1 |
a-chymotrypsin |
|
1PMC_A(6) |
Protease inhibitor LCMI II |
|
1.21 |
1591 |
|
|
info |
1GXD_A:C |
E |
1CK7_A |
proMMP2 type IV collagenase |
|
1BR9_A |
Metalloproteinase inhibitor 2 |
|
1.39 |
2445 |
|
|
info |
1HIA_AB:I |
E |
2PKA_XY |
Kallikrein |
|
1BX8_ |
Hirustatin |
|
1.4 |
1737 |
|
|
info |
1JTG_B:A |
E |
3GMU_B |
Beta-lactamase inhibitor protein |
|
1ZG4_A |
Beta-lactamase TEM-1 |
|
0.49 |
2600 |
|
|
info |
1MAH_A:F |
E |
1J06_B |
Acetylcholinesterase |
|
1FSC_ |
Fasciculin |
|
0.61 |
2145 |
|
|
info |
1N8O_ABC:E * |
E |
8GCH_A |
Chymotrypsin |
|
1IFG_A |
Ecotin |
|
0.94 |
1851 |
|
|
info |
1OC0_A:B |
E |
1B3K_A |
Plasminogen activator inhibitor-1 |
|
2JQ8_A(4) |
Vitronectin Somatomedin B domain |
|
1 |
1313 |
|
|
info |
1OPH_A:B |
E |
1QLP_A |
a-1-antitrypsin |
|
1UTQ_A |
Trypsinogen |
|
1.21 |
1360 |
|
|
info |
1OYV_B:I |
E |
1SCD_A |
Subtilisin Carlsberg |
|
1PJU_A |
Two-headed tomato inhibitor-II |
|
0.47 |
1280 |
|
|
info |
1OYV_A:I |
E |
1SCD_A |
Subtilisin Carlsberg |
|
1PJU_A |
Two-headed tomato inhibitor-II |
|
0.7 |
1930 |
|
|
info |
1PPE_E:I |
E |
1BTP_ |
Bovine trypsin |
|
1LU0_A |
CMTI-1 squash inhibitor |
|
0.44 |
1688 |
|
|
info |
1R0R_E:I |
E |
1SCN_E |
Subtilisin carlsberg |
|
2GKR_I |
OMTKY |
|
0.45 |
1409 |
|
|
info |
1TMQ_A:B |
E |
1JAE_ |
alpha-amylase |
5HP |
1B1U_A |
RAGI inhibitor |
|
0.86 |
2401 |
|
|
info |
1UDI_E:I |
E |
1UDH_ |
Uracyl-DNA glycosylase |
|
2UGI_B |
Glycosylase inhibitor |
|
0.9 |
2022 |
|
|
info |
1YVB_A:I |
E |
2GHU_A |
Falcipain 2 |
|
1CEW_I |
Cystatin |
|
0.51 |
1743 |
|
|
info |
2ABZ_B:E |
E |
3I1U_A |
Carboxypeptidase A1 |
|
1ZFI_A(1) |
Leech carboxypeptidase inhibitor |
|
0.9 |
1443 |
|
|
info |
2B42_B:A |
E |
2DCY_A |
Xylanase |
|
1T6E_X |
Xylanase inhibitor |
|
0.72 |
2520 |
|
|
info |
2J0T_A:D |
E |
966C_A |
MMP1 Intersitial collagenase |
|
1D2B_A(20) |
Metalloproteinase inhibitor 1 |
|
1.23 |
1477 |
|
|
info |
2MTA_HL:A |
E |
2BBK_JM |
Methylamine dehydrogenase |
|
2RAC_A |
Amicyanin |
|
0.41 |
1461 |
|
|
info |
2O8V_A:B |
E |
1SUR_A |
PAPS reductase |
|
2TRX_A |
Thioredoxin |
|
1.37 |
1619 |
|
|
info |
2OUL_A:B |
E |
3BPF_A |
Falcipain 2 |
|
2NNR_A |
Chagasin |
|
0.53 |
1933 |
|
|
info |
2PCC_A:B |
E |
1CCP_ |
Cyt C peroxidase |
HEM |
1YCC_ |
Cytochrome C |
HEM |
0.39 |
1141 |
|
|
info |
2SIC_E:I |
E |
1SUP_ |
Subtilisin |
|
3SSI_ |
Streptomyces subtilisin inhibitor |
|
0.36 |
1617 |
|
|
info |
2SNI_E:I |
E |
1UBN_A |
Subtilisin |
SOC |
2CI2_I |
Chymotrypsin inhibitor 2 |
|
0.35 |
1628 |
|
|
info |
2UUY_A:B |
E |
1HJ9_A |
Trypsin |
|
2UUX_A |
Tryptase inhibitor from tick |
|
0.43 |
1280 |
|
|
info |
3SGQ_E:I |
E |
2QA9_E |
Streptogrisin B |
|
2OVO_A |
Ovomucoid inhibitor third domain |
|
0.39 |
1211 |
|
|
info |
4CPA_A:I |
E |
8CPA_A |
Carboxypeptidase A |
|
1H20_A(9) |
Potato carboxypeptidase inhibitor |
|
0.62 |
1175 |
|
|
info |
7CEI_A:B |
E |
1UNK_D |
Colicin E7 nuclease |
|
1M08_B |
Im7 immunity protein |
|
0.7 |
1384 |
|
|
info |
1A2K_C:AB |
O |
1QG4_A |
Ran GTPase |
GDP |
1OUN_AB |
Nuclear transport factor 2 |
|
1.11 |
1603 |
|
|
info |
1AK4_A:D |
O |
2CPL_ |
Cyclophilin |
|
1E6J_P |
HIV capsid |
|
1.33 |
1029 |
|
|
info |
1AKJ_AB:DE |
O |
2CLR_DE |
MHC class 1 HLA-A2 |
|
1CD8_AB |
T-cell CD8 coreceptor |
|
1.14 |
1995 |
Ligand Dimer Created |
|
info |
1AZS_AB:C |
O |
1AB8_AB |
Adenylyl cyclase |
|
1AZT_A |
AC activator Gs a complex |
GSP |
0.72 |
1911 |
|
|
info |
1B6C_A:B |
O |
1D6O_A |
FKBP binding protein |
|
1IAS_A |
TGFbeta receptor |
|
1.96 |
1752 |
|
|
info |
1BUH_A:B |
O |
1HCL_ |
CDK2 kinase |
|
1DKS_A |
Ckshs1 |
|
0.75 |
1324 |
|
|
info |
1E96_A:B |
O |
1MH1_ |
Rac GTPase |
GNP |
1HH8_A |
p67 Phox |
|
0.71 |
1179 |
|
|
info |
1EFN_B:A |
O |
1AVV_A |
HIV-1-NEF protein |
|
1G83_A |
SH3 domain |
|
0.77 |
1254 |
|
|
info |
1F51_AB:E |
O |
1IXM_AB |
Sporulation response factor B |
|
1SRR_C |
Sporulation response factor F |
|
0.74 |
2407 |
|
|
info |
1FC2_C:D |
O |
1BDD_ |
Staphylococcus Protein A |
|
1FC1_AB |
Human Fc fragment |
FUC,GAL,NAG,MAN |
1.69 |
1307 |
|
|
info |
1FCC_AB:C |
O |
1FC1_AB |
Fc domain of IgG1 MO61 |
|
2IGG_A(3) |
Strep. protein G C2 fragment |
|
0.93 |
1354 |
|
|
info |
1FFW_A:B |
O |
3CHY_A |
Chemotaxis protein CheY |
|
1FWP_A |
Chemotaxis protein CheA |
|
1.43 |
1166 |
|
|
info |
1FQJ_A:B |
O |
1TND_C |
Gt-alpha |
GSP |
1FQI_A |
RGS9 |
MSE |
0.91 |
1806 |
|
|
info |
1GCQ_B:C |
O |
1GRI_B |
GRB2 C-ter SH3 domain |
|
1GCP_B |
Vav N-ter SH3 domain |
|
0.92 |
1208 |
|
|
info |
1GHQ_A:B |
O |
1C3D_ |
Complement C3 |
|
1LY2_A |
Epstein-Barr virus receptor CR2 |
|
0.34 |
800 |
|
|
info |
1GLA_G:F |
O |
1BU6_O |
Glycerol Kinase |
|
1F3Z_A |
Glucose specific phosphocarrier |
|
0.98 |
1304 |
|
|
info |
1GPW_A:B |
O |
1THF_D |
HISF protein |
|
1K9V_F |
Amidotransferase HISH |
|
0.65 |
2097 |
|
|
info |
1H9D_A:B |
O |
1EAN_A |
Runx1 domain of CBFa1 |
|
1ILF_A(1) |
Dimerisation domain of CBF-beta |
|
1.32 |
2121 |
|
|
info |
1HCF_AB:X |
O |
1B98_AM |
Neurotrophin-4 |
|
1WWB_X |
TrkB-d5 growth factor receptor |
|
0.88 |
2136 |
|
|
info |
1HE1_C:A |
O |
1MH1_ |
Rac GTPase |
GNP |
1HE9_A |
Pseudomonas toxin GAP dom. |
MES |
0.93 |
2113 |
|
|
info |
1I4D_D:AB |
O |
1MH1_ |
Rac GTPase |
GNP |
1I49_AB |
Arfaptin |
|
1.41 |
1657 |
|
|
info |
1J2J_A:B |
O |
1O3Y_A |
Arf1 GTPase |
GTP |
1OXZ_A |
GAT domain of GGA1 |
|
0.63 |
1209 |
|
|
info |
1JWH_CD:A |
O |
3EED_AB |
Casein kinase II beta chain |
|
3C13_A |
Casein kinase II a chain |
EMO |
1.27 |
1452 |
|
|
info |
1K74_AB:DE |
O |
1MZN_AB |
RXR-a |
|
1ZGY_AB |
PPAR-gamma |
|
0.8 |
2200 |
|
|
info |
1KAC_A:B |
O |
1NOB_F |
Adenovirus fiber knob protein |
|
1F5W_B |
Adenovirus receptor |
|
0.95 |
1456 |
|
|
info |
1KLU_AB:D |
O |
1H15_AB |
MHC class 2 HLA-DR1 |
|
1STE_ |
Staphylococcus enterotoxin C3 |
|
0.43 |
1254 |
|
|
info |
1KTZ_A:B |
O |
1TGK_ |
TGF-beta |
|
1M9Z_A |
TGF-beta receptor |
|
0.39 |
989 |
|
|
info |
1KXP_A:D |
O |
1IJJ_B |
Actin |
ATP |
1KW2_B |
Vitamin D binding protein |
|
1.12 |
3341 |
|
|
info |
1ML0_AB:D |
O |
1MKF_AB |
Viral chemokine binding p. M3 |
|
1DOL_ |
Chemokine Mcp1 |
|
1.02 |
2069 |
Complex Receptor Dimer Created |
|
info |
1OFU_A:XY |
O |
1OFT_AB |
SulA (PA3008) |
|
2VAW_A |
Cell division protein FtsZ |
GDP |
1.1 |
1583 |
|
|
info |
1PVH_A:B |
O |
1BQU_A |
IL6 receptor beta chain D2-D3 domains |
|
1EMR_A |
Leukemia inhibitory factor |
|
0.34 |
1403 |
|
|
info |
1QA9_A:B |
O |
1HNF_ |
CD2 |
|
1CCZ_A |
CD58 |
|
0.73 |
1353 |
|
|
info |
1RLB_ABCD:E |
O |
2PAB_ABCD |
Transthyretin |
|
1HBP_ |
Retinol binding protein |
RTL |
0.66 |
1439 |
Receptor Tetramer Created |
|
info |
1RV6_VW:X |
O |
1FZV_AB |
PIGF receptor binding domain |
|
1QSZ_A |
Flt1 protein domain 2 |
|
1.09 |
1626 |
|
|
info |
1S1Q_A:B |
O |
2F0R_A |
UEV domain |
|
1YJ1_A |
Ubiquitin |
|
0.98 |
1288 |
|
|
info |
1SBB_A:B |
O |
1BEC_ |
T-cell receptor beta |
|
1SE4_ |
Staphylococcus enterotoxin B |
|
0.37 |
1064 |
|
|
info |
1T6B_X:Y |
O |
1ACC_A |
Anthrax protective antigen |
|
1SHU_X |
Anthrax toxin receptor |
|
0.62 |
1948 |
|
|
info |
1US7_A:B |
O |
2FXS_A |
Heat shock protein 82 N-ter domain |
|
2W0G_A |
HSP 90 co-chaperone CDC37 C-ter domain |
|
1.06 |
1095 |
|
|
info |
1WDW_A:BD |
O |
1V8Z_AB |
Tryptophan synthase alpha chain 1 |
|
1GEQ_A |
Tryptophan synthase a chain |
|
1.29 |
3148 |
|
|
info |
1XD3_A:B |
O |
1UCH |
UCH-L3 |
|
1YJ1_A |
Ubiquitin |
|
1.24 |
2281 |
|
|
info |
1XU1_ABD:T |
O |
1U5Y_ABD |
TNF domain of APRIL |
|
1XUT_A(11) |
TNF receptor superfamily member 13B TACI CRD2 domain |
|
1.3 |
1697 |
|
|
info |
1Z0K_A:B |
O |
2BME_A |
Rab4A GTPase |
GNP |
1YZM_A |
RAB4 binding domain of Rabenosyn |
|
0.53 |
1787 |
|
|
info |
1Z5Y_D:E |
O |
1L6P |
N-term of DsbD |
|
2B1K_A |
E.coli CCMG protein |
|
1.23 |
1346 |
|
|
info |
1ZHH_A:B |
O |
1JX6_A |
Autoinducer 2-binding periplasmic protein LuxP |
|
2HJE_A |
Autoinducer 2 sensor kinase/phosphatase LuxQ |
|
1.31 |
2189 |
|
|
info |
1ZHI_A:B |
O |
1M4Z_A |
BAH domain of Orc1 |
|
1Z1A_A |
Sir Orc-interaction domain |
|
0.68 |
1322 |
|
|
info |
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 |
|
|
info |
2A9K_A:B |
O |
1u90_A |
Ras-related protein Ral-A |
GDP |
2C8B_X |
Mono-ADP-ribosyltransferase C3 |
|
0.85 |
1751 |
|
|
info |
2AJF_A:E |
O |
1R42_A |
ACE2 |
|
2GHV_E |
SARS spike protein receptor binding domain |
|
0.65 |
1704 |
|
|
info |
2AYO_A:B |
O |
2AYN_A |
Ubiquitin carboxyl-terminal hydrolase 14 |
|
2FCN_A |
Ubiquitin |
|
1.39 |
3027 |
|
|
info |
2B4J_AB:C |
O |
1BIZ_AB |
Integrase (HIV-1) |
|
1Z9E_A(1) |
PC4 and SFRS1 interacting protein |
|
0.99 |
1273 |
|
|
info |
2BTF_A:P |
O |
1IJJ_B |
Actin |
ATP |
1PNE_ |
Profilin |
|
0.75 |
2063 |
|
|
info |
2FJU_A:B |
O |
2ZKM_X |
Phospolipase beta 2 |
|
1MH1_A |
Rac GTPase |
GNP |
1.04 |
1245 |
|
|
info |
2G77_A:B |
O |
1FKM_A |
GTPase-activating protein GYP1 |
|
1Z06_A |
Ras-related protein Rab-33B |
GNP |
1.08 |
2524 |
|
|
info |
2HLE_A:B |
O |
2BBA_A |
Ephrin B4 receptor |
|
1IKO_P |
Ephrin B2 ectodomain |
|
1.4 |
2116 |
|
|
info |
2HQS_A:H |
O |
1CRZ_A |
TolB |
|
1OAP_A |
Pal |
|
1.14 |
2333 |
|
|
info |
2OOB_A:B |
O |
2OOA_A |
Ubiquitin ligase |
|
1YJ1_A |
Ubiquitin |
|
0.85 |
808 |
|
|
info |
2OOR_AB:C |
O |
1L7E_AB |
NAD(P) transhydrogenase subunit a part 1 |
|
1E3T_A |
NAD(P) transhydrogenase subunit beta |
NAP |
1.42 |
2065 |
|
|
info |
2VDB_A:B |
O |
3CX9_A |
Serum albumin |
|
2J5Y_A |
Peptostreptococcal albumin-binding protein |
|
0.47 |
1798 |
|
|
info |
3BP8_AB:C |
O |
1Z6R_AB |
Mlc transcription regulator |
|
3BP3_A |
PTS glucose-specific enzyme EIICB |
|
0.45 |
1391 |
|
|
info |
3D5S_A:C |
O |
1C3D_A |
Complement C3d fragment |
|
2GOM_A |
Fibrinogen-binding protein C-ter domain |
|
0.56 |
1620 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Medium Difficulty (29) |
|
|
|
|
|
|
|
|
|
info |
1BGX_HL:T |
A |
1AY1_HL |
Fab |
|
1CMW_A |
Taq polymerase |
|
1.48 |
5814 |
|
|
info |
1ACB_E:I |
E |
2CGA_B |
Chymotrypsin |
|
1EGL_ |
Eglin C |
|
2.26 |
1544 |
|
|
info |
1IJK_A:BC |
E |
1AUQ_ |
Von Willebrand Factor dom. A1 |
|
1FVU_AB |
Botrocetin |
|
0.68 |
1648 |
|
|
info |
1JIW_P:I |
E |
1AKL_A |
Alkaline metalloproteinase |
|
2RN4_A(1) |
Proteinase inhibitor |
|
2.07 |
1997 |
|
|
info |
1KKL_ABC:H |
E |
1JB1_ABC |
HPr kinase C-ter domain |
MSE |
2HPR_ |
HPr |
|
2.2 |
1641 |
Receptor Trimer Created |
|
info |
1M10_A:B |
E |
1AUQ_ |
Von willebrand factor dom. A1 |
|
1M0Z_B |
Glycoprotein IB-a |
|
2.1 |
2097 |
|
|
info |
1NW9_B:A |
E |
1JXQ_A |
Capase-9 |
|
2OPY_A |
BIR3-XPIA |
|
1.97 |
2112 |
|
|
info |
1GP2_A:BG |
O |
1GIA_ |
Gi-alpha |
GSP |
1TBG_DH |
Gi-beta,gamma |
|
1.65 |
2287 |
|
|
info |
1GRN_A:B * |
O |
1A4R_A |
CDC42 GTPase |
GDP |
1RGP_ |
CDC42 GAP |
|
1.22 |
2332 |
|
|
info |
1HE8_B:A |
O |
821P_ |
Ras GTPase |
GTN |
1E8Z_A |
PIP3 kinase |
|
0.92 |
1305 |
|
|
info |
1I2M_A:B |
O |
1QG4_A |
Ran GTPase |
GNP |
1A12_A |
RCC1 |
|
2.12 |
2779 |
|
|
info |
1IB1_AB:E |
O |
1QJB_AB |
14-3-3 protein |
|
1KUY_A |
Serotonin N-acteylase |
COT |
2.09 |
2808 |
|
|
info |
1K5D_AB:C |
O |
1RRP_AB |
Ran GTPase |
GNP |
1YRG_B |
Ran GAP |
|
1.19 |
2527 |
|
|
info |
1LFD_A:B |
O |
5P21_A |
Ras |
GNP |
1LXD_A |
RalGDS Ras-interacting domain |
|
1.79 |
1167 |
|
|
info |
1MQ8_A:B |
O |
1IAM_A |
ICAM-1 domain 1-2 |
|
1MQ9_A |
Integrin a-L I domain |
|
1.76 |
1253 |
|
|
info |
1N2C_ABCD:EF |
O |
3MIN_ABCD |
Nitrogenase Mo-Fe protein |
|
2NIP_AB |
Nitrogenase Fe protein |
|
2.13 |
3635 |
|
|
info |
1R6Q_A:C |
O |
1R6C_X |
Clp protease subunit ClpA |
|
2W9R_A |
Clp protease adaptor protein ClpS |
|
1.67 |
1651 |
|
|
info |
1SYX_A:B |
O |
1QGV_A |
Spliceosomal U5 15 kDa protein |
|
1L2Z_A(1) |
CD2 receptor binding protein 2 C-ter fragment |
|
1.64 |
1293 |
|
|
info |
1WQ1_R:G * |
O |
6Q21_D |
Ras GTPase |
GCP |
1WER_ |
Ras GAP |
|
1.16 |
2913 |
|
|
info |
1XQS_A:C |
O |
1XQR_A |
HspBP1 |
|
1S3X_A |
Hsp70 ATPase domain |
ATP |
1.77 |
2350 |
|
|
info |
1ZM4_A:B |
O |
1N0V_C |
Elongation factor 2 |
|
1XK9_A |
Diphtheria toxin A catalytic domain |
|
2.11 |
1554 |
|
|
info |
2CFH_A:C |
O |
1SZ7_A |
BET3 |
|
2BJN_A |
TPC6 |
|
1.55 |
2384 |
|
|
info |
2H7V_A:C |
O |
1MH1_ |
Rac GTPase |
GNP |
2H7O_A |
YpkA |
|
1.63 |
1574 |
|
|
info |
2HRK_A:B |
O |
2HRA_A |
Glutamyl-t-RNA synthetase |
|
2HQT_A |
GU-4 nucleic binding protein |
|
2.03 |
1595 |
|
|
info |
2J7P_A:D |
O |
1NG1_A |
SRP GTPase Ffh |
GDP |
2IYL_D |
Cell division protein FtsY |
GDP |
1.93 |
3008 |
|
|
info |
2NZ8_A:B |
O |
1MH1_ |
Rac GTPase |
GNP |
1NTY_A |
DH/PH domain of TRIO |
|
2.13 |
2599 |
|
|
info |
2OZA_B:A |
O |
3HEC_A |
MAP kinase 14 |
|
3FYK_X |
MAP kinase-activated protein kinase 2 |
|
1.89 |
6248 |
|
|
info |
2Z0E_A:B |
O |
2D1I_A |
Cysteine protease Atg4B |
|
1V49_A(1) |
Microtubule-associated proteins 1A/1B light chain 3B |
|
2.15 |
2478 |
|
|
info |
3CPH_A:G |
O |
3CPI_G |
Ras-related protein Sec4 |
|
1G16_A |
Rab GDP-dissociation inhibitor |
GNP |
2.12 |
1685 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Difficult (24) |
|
|
|
|
|
|
|
|
|
|
|
info |
1E4K_AB:C |
A |
2DTQ_AB |
FC fragment of human IgG 1 |
NAG,FUC,MAN |
1FNL_A |
Human FCGR III |
|
2.59 |
1634 |
|
|
info |
2HMI_CD:AB |
AB |
2HMI_CD |
Fab 28 |
|
1S6P_AB |
HIV1 reverse transcriptase |
|
2.26 |
1234 |
|
|
info |
1F6M_A:C |
E |
1CL0_A |
Thioredoxin reductse |
FAD |
2TIR_A |
Thioredoxin 1 |
|
4.9 |
1821 |
|
|
info |
1FQ1_A:B |
E |
1B39_A |
CDK2 kinase |
ATP,ACE |
1FPZ_F |
CDK inhibitor 3 |
|
3.41 |
1832 |
|
|
info |
1PXV_A:C |
E |
1X9Y_A |
Cystein protease |
|
1NYC_A |
Cystein protease inhibitor |
|
2.63 |
2336 |
|
|
info |
1ZLI_A:B |
E |
1KWM_A |
Carboxypeptidase B |
|
2JTO_A(6) |
Tick carboxypeptidase inhibitor |
|
2.53 |
2084 |
|
|
info |
2O3B_A:B |
E |
1ZM8_A |
NucA nuclease |
|
1J57_A |
NuiA nuclease inhibitor |
|
3.13 |
1675 |
|
|
info |
1ATN_A:D |
O |
1IJJ_B |
Actin |
ATP |
3DNI_ |
Dnase I |
|
3.28 |
1774 |
|
|
info |
1BKD_R:S |
O |
1CTQ_A |
Ras GTPase |
1GNP |
2II0_A |
Son of sevenless |
|
2.86 |
3163 |
|
|
info |
1DE4_AB:CF |
O |
1A6Z_AB |
beta2-microglobulin |
|
1CX8_AB |
Transferrin receptor ectodom. |
|
2.59 |
2066 |
|
|
info |
1EER_A:BC |
O |
1BUY_A |
Erythropoietin |
|
1ERN_AB |
EPO receptor |
|
2.44 |
3347 |
Ligand Dimer Created |
|
info |
1FAK_HL:T |
O |
1QFK_HL |
Coagulation factor VIIa |
|
1TFH_B |
Soluble tissue factor |
|
6.18 |
3363 |
|
|
info |
1H1V_A:G |
O |
1IJJ_B |
Actin |
ATP |
1D0N_B |
Gelsolin |
|
6.62 |
2071 |
|
|
info |
1IBR_A:B |
O |
1QG4_A |
Ran GTPase |
GDP |
1F59_A |
Importin beta |
|
2.54 |
2270 |
|
|
info |
1IRA_Y:X |
O |
1G0Y_R |
Interleukin-1 receptor |
|
1ILR_1 |
Interleukin-1 receptor antagonist protein |
|
8.38 |
3367 |
|
|
info |
1JK9_A:B |
O |
1QUP_A |
CCS metallochaperone |
|
2JCW_A |
SOD1 superoxide dismutase |
|
2.51 |
2130 |
|
|
info |
1JMO_A:HL |
O |
1JMJ_A |
Heparin cofactor |
|
2CN0_HL |
Thrombin |
|
3.21 |
3461 |
|
|
info |
1JZD_AB:C |
O |
1JZO_AB |
DsbC disurfide bond isomerase |
|
1JPE_A |
DsbD disulfide bond isomerase |
|
2.71 |
2026 |
|
|
info |
1R8S_A:E |
O |
1HUR_A |
Arf1 GTPase |
GDP |
1R8M_E |
Sec 7 domain |
|
3.73 |
2986 |
|
|
info |
1Y64_A:B |
O |
2FXU_A |
Actin |
ATP |
1UX5_A |
BNI1 protein |
|
4.69 |
2745 |
|
|
info |
2C0L_A:B |
O |
1FCH_A |
PTS1 and TRP region of PEX5 |
|
1C44_A |
SCP2 |
|
2.62 |
2013 |
|
|
info |
2I9B_A:E |
O |
1YWH_A |
Urokinase plasminogen activator surface receptor |
|
2I9A_A |
Urokinase-type plasminogen activator |
|
3.79 |
2371 |
|
|
info |
2IDO_A:B |
O |
1J54_A |
DNA polymerase III e exonuclease domain |
|
1SE7_A(1) |
HOT protein (P1 phage) |
|
2.79 |
1953 |
|
|
info |
2OT3_B:A |
O |
1YZU_A |
Rab21 GTPase |
GNP |
1TXU_A |
Rabex-5 VPS9 domain |
|
2.79 |
2306 |
|
|
|
|
|
a Complex category labels: |
|
|
|
|
E = Enzyme/Inhibitor or
Enzyme/Substrate |
|
|
|
|
A = Antibody/Antigen |
|
|
|
|
O = Others |
|
|
|
|
AB = Antigen/Bound
Antibody |
|
|
|
b RMSD of Ca atoms of interface residues calculated after finding
the best superposition of bound and unbound interfaces. |
|
|
|
c Change in Accessible Surface Area upon complex formation
calculated using NACCESS. |
|
|
|
|
|
|
|
|
HETATMs
column lists cofactors and small ligands present in the downloadable
cleaned-up files. |
|
|
|
|
We
included those small molecules important for binding and other compounds on
surfaces. |
|
|
|
|
Glycosylations
not crucial for binding were excluded.
|
|
|
|
Multimer column contains
comments pertaining to any multimers created by symmetry prior to docking |
|
|
|
|
if
the asymmetric unit did not contain the full biologically relevant
molecule. |
|
|
|
|
|
|
|
* Cases marked with the
asterisk are those that would be considered redundant under the SCOP
Superfamily-Superfamily |
|
|
|
|
|
pair non-redundancy
criterion. |
|
|
|
|
|
|
? Please follow the "+info" link
for more information on those cases |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|