Structure of PDB 1ubt Chain S Binding Site BS03

Receptor Information
>1ubt Chain S (length=267) Species: 883 (Nitratidesulfovibrio vulgaris str. 'Miyazaki F') [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LMGPRRPSVVYLHNAECTGCSESVLRAFEPYIDTLILDTLSLDYHETIMA
AAGDAAEAALEQAVNSPHGFIAVVEGGIPTAANGIYGKVANHTMLDICSR
ILPKAQAVIAYGTCATFGGVQAAKPNPTGAKGVNDALKHLGVKAINIAGC
PPNPYNLVGTIVYYLKNKAAPELDSLNRPTMFFGQTVHEQCPRLPHFDAG
EFAPSFESEEARKGWCLYELGCKGPVTMNNCPKIKFNQTNWPVDAGHPCI
GCSEPDFWDAMTPFYQN
Ligand information
Ligand IDF3S
InChIInChI=1S/3Fe.4S
InChIKeyFCXHZBQOKRZXKS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385S1[Fe]S[Fe]2S[Fe]1S2
OpenEye OEToolkits 2.0.7S1[Fe]2S[Fe]3[S]2[Fe]1S3
FormulaFe3 S4
NameFE3-S4 CLUSTER
ChEMBL
DrugBank
ZINC
PDB chain1ubt Chain S Residue 1003 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1ubt Structural Studies of the Carbon Monoxide Complex of [NiFe]hydrogenase from Desulfovibrio vulgaris Miyazaki F: Suggestion for the Initial Activation Site for Dihydrogen
Resolution1.34 Å
Binding residue
(original residue number in PDB)		N229 C231 F236 W241 P242 C249 I250 C252
Binding residue
(residue number reindexed from 1)		N229 C231 F236 W241 P242 C249 I250 C252
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) C222 C231
Catalytic site (residue number reindexed from 1) C222 C231
Enzyme Commision number 1.12.2.1: cytochrome-c3 hydrogenase.
Gene Ontology
Molecular Function
GO:0008901 ferredoxin hydrogenase activity
GO:0009055 electron transfer activity
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
GO:0047806 cytochrome-c3 hydrogenase activity
GO:0051536 iron-sulfur cluster binding
GO:0051538 3 iron, 4 sulfur cluster binding
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0009061 anaerobic respiration
Cellular Component
GO:0009375 ferredoxin hydrogenase complex
GO:0016020 membrane
GO:0042597 periplasmic space
GO:0044569 [Ni-Fe] hydrogenase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1ubt, PDBe:1ubt, PDBj:1ubt
PDBsum1ubt
PubMed12296727
UniProtP21853|PHNS_NITV9 Periplasmic [NiFe] hydrogenase small subunit (Gene Name=hydA)

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