4KO4

High X-ray dose 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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth S]	d4ko4s_	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)
C [auth T]	d4ko4t_	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)
B [auth L]	d4ko4l_	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)
D [auth M]	d4ko4m_	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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth S]	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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth S]	Oxidored_q6	e4ko4S1	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 [auth S]	NiFe_hyd_SSU_C	e4ko4S2	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)
C [auth T]	Oxidored_q6	e4ko4T1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Oxidored_q6	ECOD (1.6)
C [auth T]	NiFe_hyd_SSU_C	e4ko4T2	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 [auth L]	NiFeSe_Hases_2nd	e4ko4L1	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 [auth L]	NiFeSe_Hases_1st	e4ko4L2	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 [auth L]	NiFeSe_Hases_3rd	e4ko4L3	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 [auth L]	NiFeSe_Hases_3rd_1	e4ko4L4	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)
D [auth M]	NiFeSe_Hases_2nd	e4ko4M1	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)
D [auth M]	NiFeSe_Hases_1st	e4ko4M2	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)
D [auth M]	NiFeSe_Hases_3rd	e4ko4M3	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)
D [auth M]	NiFeSe_Hases_3rd_1	e4ko4M4	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 [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)
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)
B [auth L]	1.10.645.10	Mainly Alpha	Orthogonal Bundle	Cytochrome-c3 Hydrogenase	chain B	CATH (4.3.0)
D [auth M]	1.10.645.10	Mainly Alpha	Orthogonal Bundle	Cytochrome-c3 Hydrogenase	chain B	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth S], C [auth T]	PF14720	NiFe/NiFeSe hydrogenase small subunit C-terminal (NiFe_hyd_SSU_C)	NiFe/NiFeSe hydrogenase small subunit C-terminal	-	Family
A [auth S], C [auth T]	PF01058	NADH ubiquinone oxidoreductase, 20 Kd subunit (Oxidored_q6)	NADH ubiquinone oxidoreductase, 20 Kd subunit	-	Family
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
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 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 [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 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 [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]	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
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

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.