Structure of PDB 5y4n Chain S Binding Site BS03

Receptor Information
>5y4n 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 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 chain5y4n Chain S Residue 1003 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5y4n Ni-elimination from the active site of the standard [NiFe]‐hydrogenase upon oxidation by O2.
Resolution1.69 Å
Binding residue
(original residue number in PDB)		N229 C231 F236 W241 P242 C249 I250 C252
Binding residue
(residue number reindexed from 1)		N226 C228 F233 W238 P239 C246 I247 C249
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5y4n, PDBe:5y4n, PDBj:5y4n
PDBsum5y4n
PubMed28967475
UniProtP21853|PHNS_NITV9 Periplasmic [NiFe] hydrogenase small subunit (Gene Name=hydA)

[Back to BioLiP]