6RTP

THE 3D STRUCTURE OF [NIFESE] HYDROGENASE G50T VaRIANT FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH AT 1.10 ANGSTROM RESOLUTION

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
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)
A	d6rtpa_	Multi-domain proteins (alpha and beta)	HydA/Nqo6-like	HydA/Nqo6-like	Nickel-iron hydrogenase, small subunit	automated matches	(Nitratidesulfovibrio vulgaris str. Hildenborough ) [TaxId: 882 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	HydB/Nqo4-like	8077217	3001849	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Oxidored_q6	e6rtpA1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Oxidored_q6	ECOD (1.6)
A	NiFe_hyd_SSU_C	e6rtpA2	A: few secondary structure elements	X: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit (From Topology)	H: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit (From Topology)	T: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit	F: NiFe_hyd_SSU_C	ECOD (1.6)
B	NiFeSe_Hases_2nd	e6rtpB3	A: beta meanders	X: all-beta domain in nickel-iron hydrogenase large subunit (From Topology)	H: all-beta domain in nickel-iron hydrogenase large subunit (From Topology)	T: all-beta domain in nickel-iron hydrogenase large subunit	F: NiFeSe_Hases_2nd	ECOD (1.6)
B	NiFeSe_Hases_1st	e6rtpB4	A: alpha complex topology	X: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)	H: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)	T: alpha-helical domain in nickel-iron hydrogenase, large subunit	F: NiFeSe_Hases_1st	ECOD (1.6)
B	NiFeSe_Hases_3rd	e6rtpB2	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)	T: Ni-Fe binding domain in nickel-iron hydrogenase large subunit	F: NiFeSe_Hases_3rd	ECOD (1.6)
B	NiFeSe_Hases_3rd_1	e6rtpB1	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)	T: Ni-Fe binding domain in nickel-iron hydrogenase large subunit	F: NiFeSe_Hases_3rd_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF14720	NiFe/NiFeSe hydrogenase small subunit C-terminal (NiFe_hyd_SSU_C)	NiFe/NiFeSe hydrogenase small subunit C-terminal	-	Family
A	PF01058	NADH ubiquinone oxidoreductase, 20 Kd subunit (Oxidored_q6)	NADH ubiquinone oxidoreductase, 20 Kd subunit	-	Family
B	PF00374	Nickel-dependent hydrogenase (NiFeSe_Hases)	Nickel-dependent hydrogenase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Periplasmic [NiFeSe] hydrogenase, 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 oxidoreductase activity, acting on hydrogen as donor, cytochrome as acceptor cytochrome-c3 hydrogenase activity 4 iron, 4 sulfur cluster binding 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 oxidoreductase activity, acting on hydrogen as donor, cytochrome as acceptor cytochrome-c3 hydrogenase activity 4 iron, 4 sulfur cluster binding cation binding ion binding metal ion binding	-	protein-containing complex catalytic complex oxidoreductase complex ferredoxin hydrogenase complex intracellular protein-containing complex periplasmic space cellular anatomical entity
B	Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing	cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule 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 4 iron, 4 sulfur cluster binding cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule 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 4 iron, 4 sulfur cluster binding metal cluster binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR006311	Twin-arginine translocation pathway, signal sequence	Conserved Site
A	IPR001821	[NiFe]-hydrogenase, small subunit	Family
A	IPR027394	Cytochrome-c3 hydrogenase, C-terminal	Domain
A	IPR006137	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	Domain
A	IPR037024	[NiFe]-hydrogenase, small subunit, N-terminal domain superfamily	Homologous Superfamily
A	IPR019546	Twin-arginine translocation pathway, signal sequence, bacterial/archaeal	Conserved Site
A	IPR037148	[NiFe]-hydrogenase, small subunit, C-terminal domain superfamily	Homologous Superfamily
B	IPR001501	Nickel-dependent hydrogenase, large subunit	Family
B	IPR029014	[NiFe]-hydrogenase, large subunit	Homologous Superfamily
B	IPR018194	Nickel-dependent hydrogenase, large subunit, nickel binding site	Binding Site

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	CSD	Parent Component: CYS RESID: AA0262 PSI-MOD : L-cysteine sulfinic acid MOD:00267

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.