Structure of PDB 5xlf Chain S Binding Site BS02

Receptor Information
>5xlf Chain S (length=264) Species: 883 (Nitratidesulfovibrio vulgaris str. 'Miyazaki F') [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PRRPSVVYLHNAECTGCSESVLRAFEPYIDTLILDTLSLDYHETIMAAAG
DAAEAALEQAVNSPHGFIAVVEGGIPTAANGIYGKVANHTMLDICSRILP
KAQAVIAYGTCATFGGVQAAKPNPTGAKGVNDALKHLGVKAINIAGCPPN
PYNLVGTIVYYLKNKAAPELDSLNRPTMFFGQTVHEQCPRLPHFDAGEFA
PSFESEEARKGWCLYELGCKGPVTMNNCPKIKFNQTNWPVDAGHPCIGCS
EPDFWDAMTPFYQN
Ligand information
Ligand IDSF4
InChIInChI=1S/4Fe.4S
InChIKeyLJBDFODJNLIPKO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7[S]12[Fe]3[S]4[Fe]1[S]5[Fe]2[S]3[Fe]45
CACTVS 3.385S1[Fe]S[Fe]1.S2[Fe]S[Fe]2
FormulaFe4 S4
NameIRON/SULFUR CLUSTER
ChEMBL
DrugBank
ZINC
PDB chain5xlf Chain S Residue 1002 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5xlf Ni-elimination from the active site of the standard [NiFe]‐hydrogenase upon oxidation by O2.
Resolution1.71 Å
Binding residue
(original residue number in PDB)		H188 C191 R193 L194 C216 L217 C222
Binding residue
(residue number reindexed from 1)		H185 C188 R190 L191 C213 L214 C219
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) C17 C20 C114 C150 H188 C191 C216 C222 C231 P242 C249 C252
Catalytic site (residue number reindexed from 1) C14 C17 C111 C147 H185 C188 C213 C219 C228 P239 C246 C249
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:5xlf, PDBe:5xlf, PDBj:5xlf
PDBsum5xlf
PubMed28967475
UniProtP21853|PHNS_NITV9 Periplasmic [NiFe] hydrogenase small subunit (Gene Name=hydA)

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