Structure of PDB 5y4n Chain S

Receptor sequence
>5y4nS (length=264) Species: 883 (Nitratidesulfovibrio vulgaris str. 'Miyazaki F') [Search protein sequence]
PRRPSVVYLHNAECTGCSESVLRAFEPYIDTLILDTLSLDYHETIMAAAG
DAAEAALEQAVNSPHGFIAVVEGGIPTAANGIYGKVANHTMLDICSRILP
KAQAVIAYGTCATFGGVQAAKPNPTGAKGVNDALKHLGVKAINIAGCPPN
PYNLVGTIVYYLKNKAAPELDSLNRPTMFFGQTVHEQCPRLPHFDAGEFA
PSFESEEARKGWCLYELGCKGPVTMNNCPKIKFNQTNWPVDAGHPCIGCS
EPDFWDAMTPFYQN
3D structure
PDB5y4n Ni-elimination from the active site of the standard [NiFe]‐hydrogenase upon oxidation by O2.
ChainS
Resolution1.69 Å
3D
structure
Catalytic site residues are labeled in the structure
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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.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 SF4 S E16 C17 C20 G112 C114 C150 P151 E13 C14 C17 G109 C111 C147 P148
BS02 SF4 S H188 C191 R193 L194 C216 L217 C222 H185 C188 R190 L191 C213 L214 C219
BS03 F3S S N229 C231 F236 W241 P242 C249 I250 C252 N226 C228 F233 W238 P239 C246 I247 C249
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:5y4n, PDBe:5y4n, PDBj:5y4n
PDBsum5y4n
PubMed28967475
UniProtP21853|PHNS_NITV9 Periplasmic [NiFe] hydrogenase small subunit (Gene Name=hydA)

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