Structure of PDB 3kfk Chain A Binding Site BS01

Receptor Information

>3kfk Chain A (length=487) Species: 39152 (Methanococcus maripaludis)

NMKRYMGRDAQRMNILAGRIIAETVRSTLGPKGMDKMLVDDLGDVVVTND
GVTILREMSVEHPAAKMLIEVAKTQEKEVGDGTTTAVVVAGELLRKAEEL
LDQNVHPTIVVKGYQAAAQKAQELLKTIACEVGAQDKEILTKIAMTSITG
KGAEKAKEKLAEIIVEAVSAVVDDEGKVDKDLIKIEKKSGASIDDTELIK
GVLVDKERVSAQMPKKVTDAKIALLNCAIEETASEMLKDMVAEIKASGAN
VLFCQKGIDDLAQHYLAKEGIVAARRVKKSDMEKLAKATGANVITNIKDL
SAQDLGDAGLVEERKISGDSMIFVEECKHPKAVTMLIRGTTEHVIEEVAR
AVDDAVGVVGCTIEDGRIVSGGGSTEVELSMKLREYAEGISGREQLAVRA
FADALEVIPRTLAENAGLDAIEILVKVRAAHASNGNKCAGLNVFTGAVED
MCENGVVEPLRVKTQAIQSAAESTEMLLRIDDVIAAE

Ligand information

• Ligand ID: AGS
• InChI: InChI=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
• InChIKey: NLTUCYMLOPLUHL-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
  CACTVS 3.370: Nc1ncnc2n(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 3.370: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O
  OpenEye OEToolkits 1.7.6: c1nc(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 12.01: O=P(O)(OP(=S)(O)O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
• Formula: C10 H16 N5 O12 P3 S
• Name: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER;
  ATP-GAMMA-S;
  ADENOSINE 5'-(3-THIOTRIPHOSPHATE);
  ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);
  ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE
• ChEMBL: CHEMBL131890
• DrugBank: DB02930
• ZINC: ZINC000008295128
• PDB chain: 3kfk Chain A Residue 544

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3kfk Crystal structures of a group II chaperonin reveal the open and closed states associated with the protein folding cycle.
• Resolution: 6.003 Å
• Binding residue (original residue number in PDB): L39 G40 P41 D60 D91 T93 T94 T95 G403 G404 E490
• Binding residue (residue number reindexed from 1): L29 G30 P31 D50 D81 T83 T84 T85 G371 G372 E458
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): D60 T93 T94 D386
• Catalytic site (residue number reindexed from 1): D50 T83 T84 D354

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

External links

• PDB: RCSB:3kfk, PDBe:3kfk, PDBj:3kfk
• PDBsum: 3kfk
• PubMed: 20573955
• UniProt: Q877G8