Structure of PDB 3kfk Chain D Binding Site BS01

Receptor Information
>3kfk Chain D (length=484) Species: 39152 (Methanococcus maripaludis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NMKRYMGRDAQRMNILAGRIIAETVRSTLGPKGMDKMLVDDLGDVVVTND
GVTILREMSVEHPAAKMLIEVAKTQEKEVGDGTTTAVVVAGELLRKAEEL
LDQNVHPTIVVKGYQAAAQKAQELLKTIACEVGAQDKEILTKIAMTSITG
KGAEKAKEKLAEIIVEAVSAVVDDEGKVDKDLIKIEKKSGASIDDTELVL
VDKERVSAQMPKKVTDAKIALLNCAIEETASEMLKDMVAEIKASGANVLF
CQKGIDDLAQHYLAKEGIVAARRVKKSDMEKLAKATGANVITNIKDLSAQ
DLGDAGLVEERKISGDSMIFVEECKHPKAVTMLIRGTTEHVIEEVARAVD
DAVGVVGCTIEDGRIVSGGGSTEVELSMKLREYAEGISGREQLAVRAFAD
ALEVIPRTLAENAGLDAIEILVKVRAAHASNGNKCAGLNVFTGAVEDMCE
NGVVEPLRVKTQAIQSAAESTEMLLRIDDVIAAE
Ligand information
Ligand IDAGS
InChIInChI=1S/C10H16N5O12P3S/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(25-10)1-24-28(18,19)26-29(20,21)27-30(22,23)31/h2-4,6-7,10,16-17H,1H2,(H,18,19)(H,20,21)(H2,11,12,13)(H2,22,23,31)/t4-,6-,7-,10-/m1/s1
InChIKeyNLTUCYMLOPLUHL-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[C@@H](O)[C@H]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
ACDLabs 12.01O=P(O)(OP(=S)(O)O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC10 H16 N5 O12 P3 S
NamePHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER;
ATP-GAMMA-S;
ADENOSINE 5'-(3-THIOTRIPHOSPHATE);
ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);
ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE
ChEMBLCHEMBL131890
DrugBankDB02930
ZINCZINC000008295128
PDB chain3kfk Chain D Residue 544 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3kfk Crystal structures of a group II chaperonin reveal the open and closed states associated with the protein folding cycle.
Resolution6.003 Å
Binding residue
(original residue number in PDB)		D60 D91 G92 T93 G403 G404 V488 E490
Binding residue
(residue number reindexed from 1)		D50 D81 G82 T83 G368 G369 V453 E455
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) D60 T93 T94 D386
Catalytic site (residue number reindexed from 1) D50 T83 T84 D351
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016887 ATP hydrolysis activity
GO:0042802 identical protein binding
GO:0046872 metal ion binding
GO:0051082 unfolded protein binding
GO:0140662 ATP-dependent protein folding chaperone
Biological Process
GO:0006457 protein folding

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3kfk, PDBe:3kfk, PDBj:3kfk
PDBsum3kfk
PubMed20573955
UniProtQ877G8

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