4KL8 | pdb_00004kl8

High-resolution structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D [auth M]	d4kl8m_	Multi-domain proteins (alpha and beta)	HydB/Nqo4-like	HydB/Nqo4-like	Nickel-iron hydrogenase, large subunit	automated matches	(Desulfomicrobium baculatum DSM 4028 ) [TaxId: 525897 ],	SCOPe (2.08)
B [auth L]	d4kl8l_	Multi-domain proteins (alpha and beta)	HydB/Nqo4-like	HydB/Nqo4-like	Nickel-iron hydrogenase, large subunit	automated matches	(Desulfomicrobium baculatum DSM 4028 ) [TaxId: 525897 ],	SCOPe (2.08)
C [auth T]	d4kl8t_	Multi-domain proteins (alpha and beta)	HydA/Nqo6-like	HydA/Nqo6-like	Nickel-iron hydrogenase, small subunit	automated matches	(Desulfomicrobium baculatum ) [TaxId: 899 ],	SCOPe (2.08)
A [auth S]	d4kl8s_	Multi-domain proteins (alpha and beta)	HydA/Nqo6-like	HydA/Nqo6-like	Nickel-iron hydrogenase, small subunit	automated matches	(Desulfomicrobium baculatum ) [TaxId: 899 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth T]	SCOP2B Superfamily	Nqo6/HydA N-terminal domain-like	8054421	3002291	SCOP2B (2022-06-29)
C [auth T]	SCOP2B Superfamily	HydA C-terminal domain-like	8037590	3001861	SCOP2B (2022-06-29)
A [auth S]	SCOP2B Superfamily	Nqo6/HydA N-terminal domain-like	8054421	3002291	SCOP2B (2022-06-29)
A [auth S]	SCOP2B Superfamily	HydA C-terminal domain-like	8037590	3001861	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)
D [auth M]	STK_08120-like	e4kl8M1	A: alpha bundles	X: PBZ domain	H: PBZ domain	T: PBZ domain	F: STK_08120-like	ECOD (develop294)
B [auth L]	STK_08120-like	e4kl8L1	A: alpha bundles	X: PBZ domain	H: PBZ domain	T: PBZ domain	F: STK_08120-like	ECOD (develop294)
C [auth T]	STK_08120-like	e4kl8T1	A: alpha bundles	X: PBZ domain	H: PBZ domain	T: PBZ domain	F: STK_08120-like	ECOD (develop294)
A [auth S]	STK_08120-like	e4kl8S1	A: alpha bundles	X: PBZ domain	H: PBZ domain	T: PBZ domain	F: STK_08120-like	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth L], D [auth M]	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
B [auth L], D [auth M]	Nickel-dependent hydrogenase large subunit	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	-	cellular anatomical structure periplasmic space
A [auth S], C [auth T]	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 hydrogenase (acceptor) activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding electron transfer activity cation binding ion 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 hydrogenase (acceptor) activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule 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	cellular anatomical structure membrane protein-containing complex catalytic complex oxidoreductase complex ferredoxin hydrogenase complex intracellular protein-containing complex [Ni-Fe] hydrogenase complex periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth L], D [auth M]	IPR001501	Nickel-dependent hydrogenase, large subunit	Family
B [auth L], D [auth M]	IPR029014	[NiFe]-hydrogenase, large subunit	Homologous Superfamily
B [auth L], D [auth M]	IPR018194	Nickel-dependent hydrogenase, large subunit, nickel binding site	Binding Site
B [auth L], D [auth M]	IPR050867	[NiFe]/[NiFeSe] hydrogenase large subunit	Family
A [auth S], C [auth T]	IPR006311	Twin-arginine translocation pathway, signal sequence	Conserved Site
A [auth S], C [auth T]	IPR001821	[NiFe]-hydrogenase, small subunit	Family
A [auth S], C [auth T]	IPR027394	Cytochrome-c3 hydrogenase, C-terminal	Domain
A [auth S], C [auth T]	IPR006137	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	Domain
A [auth S], C [auth T]	IPR053622	NiFe/NiFeSe hydrogenase small subunit	Family
A [auth S], C [auth T]	IPR037024	[NiFe]-hydrogenase, small subunit, N-terminal domain superfamily	Homologous Superfamily
A [auth S], C [auth T]	IPR019546	Twin-arginine translocation pathway, signal sequence, bacterial/archaeal	Conserved Site
A [auth S], C [auth T]	IPR037148	[NiFe]-hydrogenase, small subunit, C-terminal domain superfamily	Homologous Superfamily

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.