5XVC | pdb_00005xvc

[NiFe]-hydrogenase (Hyb-type) from Citrobacter sp. S-77 in a ferricyanide-oxidized condition

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D [auth T]	d5xvct_	Multi-domain proteins (alpha and beta)	HydA/Nqo6-like	HydA/Nqo6-like	automated matches	automated matches	(Citrobacter sp. S-77 ) [TaxId: 1080067 ],	SCOPe (2.08)
B [auth S]	d5xvcs_	Multi-domain proteins (alpha and beta)	HydA/Nqo6-like	HydA/Nqo6-like	automated matches	automated matches	(Citrobacter sp. S-77 ) [TaxId: 1080067 ],	SCOPe (2.08)
C [auth M]	d5xvcm_	Multi-domain proteins (alpha and beta)	HydB/Nqo4-like	HydB/Nqo4-like	automated matches	automated matches	(Citrobacter sp. S-77 ) [TaxId: 1080067 ],	SCOPe (2.08)
A [auth L]	d5xvcl_	Multi-domain proteins (alpha and beta)	HydB/Nqo4-like	HydB/Nqo4-like	automated matches	automated matches	(Citrobacter sp. S-77 ) [TaxId: 1080067 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D [auth T]	e5xvcT1	A: L-aspartase middle domain-like	X: gp11/gp12 receptor-binding domain	H: gp11/gp12 receptor-binding domain	T: Chlorophyllase2	F:	ECOD (20:10:01)
B [auth S]	e5xvcS1	A: L-aspartase middle domain-like	X: gp11/gp12 receptor-binding domain	H: gp11/gp12 receptor-binding domain	T: Chlorophyllase2	F:	ECOD (20:10:01)
C [auth M]	e5xvcM1	A: L-aspartase middle domain-like	X: gp11/gp12 receptor-binding domain	H: gp11/gp12 receptor-binding domain	T: Chlorophyllase2	F:	ECOD (20:10:01)
A [auth L]	e5xvcL1	A: L-aspartase middle domain-like	X: gp11/gp12 receptor-binding domain	H: gp11/gp12 receptor-binding domain	T: Chlorophyllase2	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth T]	3.40.50.700	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	CATH (4.3.0)
D [auth T]	4.10.480.10	Few Secondary Structures	Irregular	Cytochrome-c3 Hydrogenase	Chain A, domain 2	CATH (4.3.0)
B [auth S]	3.40.50.700	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	CATH (4.3.0)
B [auth S]	4.10.480.10	Few Secondary Structures	Irregular	Cytochrome-c3 Hydrogenase	Chain A, domain 2	CATH (4.3.0)
C [auth M]	1.10.645.10	Mainly Alpha	Orthogonal Bundle	Cytochrome-c3 Hydrogenase	chain B	CATH (4.3.0)
A [auth L]	1.10.645.10	Mainly Alpha	Orthogonal Bundle	Cytochrome-c3 Hydrogenase	chain B	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth S], D [auth T]	[NiFe]-hydrogenase 2 small subunit	oxidoreductase activity oxidoreductase activity, acting on hydrogen as donor, iron-sulfur protein as acceptor oxidoreductase activity, acting on hydrogen as donor ferredoxin hydrogenase activity catalytic activity iron-sulfur cluster binding binding 3 iron, 4 sulfur cluster binding metal cluster binding small molecule binding hydrogenase (acceptor) activity 4 iron, 4 sulfur cluster binding electron transfer activity cation binding oxidoreductase activity oxidoreductase activity, acting on hydrogen as donor, iron-sulfur protein as acceptor oxidoreductase activity, acting on hydrogen as donor ferredoxin hydrogenase activity catalytic activity iron-sulfur cluster binding binding 3 iron, 4 sulfur cluster binding metal cluster binding small molecule binding hydrogenase (acceptor) activity 4 iron, 4 sulfur cluster binding electron transfer activity cation binding ion binding metal ion binding	cellular respiration energy derivation by oxidation of organic compounds metabolic process cellular process generation of precursor metabolites and energy anaerobic respiration	protein-containing complex catalytic complex oxidoreductase complex ferredoxin hydrogenase complex intracellular protein-containing complex [Ni-Fe] hydrogenase complex cell periphery cellular anatomical structure plasma membrane membrane periplasmic space
A [auth L], C [auth M]	[NiFe]-hydrogenase 2 large subunit	hydrogenase (acceptor) activity oxidoreductase activity oxidoreductase activity, acting on hydrogen as donor catalytic activity cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding oxidoreductase activity, acting on hydrogen as donor, iron-sulfur protein as acceptor ferredoxin hydrogenase activity	-	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth S], D [auth T]	IPR001821	[NiFe]-hydrogenase, small subunit	Family
B [auth S], D [auth T]	IPR027394	Cytochrome-c3 hydrogenase, C-terminal	Domain
B [auth S], D [auth T]	IPR006137	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	Domain
B [auth S], D [auth T]	IPR037024	[NiFe]-hydrogenase, small subunit, N-terminal domain superfamily	Homologous Superfamily
B [auth S], D [auth T]	IPR037148	[NiFe]-hydrogenase, small subunit, C-terminal domain superfamily	Homologous Superfamily
A [auth L], C [auth M]	IPR001501	Nickel-dependent hydrogenase, large subunit	Family
A [auth L], C [auth M]	IPR029014	[NiFe]-hydrogenase, large subunit	Homologous Superfamily
A [auth L], C [auth M]	IPR018194	Nickel-dependent hydrogenase, large subunit, nickel binding site	Binding Site
A [auth L], C [auth M]	IPR050867	[NiFe]/[NiFeSe] hydrogenase large subunit	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A [auth L], C [auth M]	CSO	Parent Component: CYS RESID: AA0205 PSI-MOD : L-cysteine sulfenic acid MOD:00210

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

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