5AA5 | pdb_00005aa5

Actinobacterial-type NiFe-hydrogenase from Ralstonia eutropha H16 at 2.85 Angstrom resolution

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
K [auth L]	d5aa5l_	Multi-domain proteins (alpha and beta)	HydB/Nqo4-like	HydB/Nqo4-like	automated matches	automated matches	(Cupriavidus necator H16 ) [TaxId: 381666 ],	SCOPe (2.08)
J [auth K]	d5aa5k_	Multi-domain proteins (alpha and beta)	HydB/Nqo4-like	HydB/Nqo4-like	automated matches	automated matches	(Cupriavidus necator H16 ) [TaxId: 381666 ],	SCOPe (2.08)
I	d5aa5i_	Multi-domain proteins (alpha and beta)	HydB/Nqo4-like	HydB/Nqo4-like	automated matches	automated matches	(Cupriavidus necator H16 ) [TaxId: 381666 ],	SCOPe (2.08)
G	d5aa5g_	Multi-domain proteins (alpha and beta)	HydB/Nqo4-like	HydB/Nqo4-like	automated matches	automated matches	(Cupriavidus necator H16 ) [TaxId: 381666 ],	SCOPe (2.08)
E	d5aa5e_	Multi-domain proteins (alpha and beta)	HydB/Nqo4-like	HydB/Nqo4-like	automated matches	automated matches	(Cupriavidus necator H16 ) [TaxId: 381666 ],	SCOPe (2.08)
C	d5aa5c_	Multi-domain proteins (alpha and beta)	HydB/Nqo4-like	HydB/Nqo4-like	automated matches	automated matches	(Cupriavidus necator H16 ) [TaxId: 381666 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
K [auth L]	Carb_anhydrase	e5aa5L1	A: alpha bundles	X: ACP-like	H: Acyl-carrier protein (ACP)	T: Acyl-carrier protein (ACP)	F: Carb_anhydrase	ECOD (develop294)
J [auth K]	Carb_anhydrase	e5aa5K1	A: alpha bundles	X: ACP-like	H: Acyl-carrier protein (ACP)	T: Acyl-carrier protein (ACP)	F: Carb_anhydrase	ECOD (develop294)
I	Carb_anhydrase	e5aa5I1	A: alpha bundles	X: ACP-like	H: Acyl-carrier protein (ACP)	T: Acyl-carrier protein (ACP)	F: Carb_anhydrase	ECOD (develop294)
G	Carb_anhydrase	e5aa5G1	A: alpha bundles	X: ACP-like	H: Acyl-carrier protein (ACP)	T: Acyl-carrier protein (ACP)	F: Carb_anhydrase	ECOD (develop294)
E	Carb_anhydrase	e5aa5E2	A: alpha bundles	X: ACP-like	H: Acyl-carrier protein (ACP)	T: Acyl-carrier protein (ACP)	F: Carb_anhydrase	ECOD (develop294)
C	Carb_anhydrase	e5aa5C1	A: alpha bundles	X: ACP-like	H: Acyl-carrier protein (ACP)	T: Acyl-carrier protein (ACP)	F: Carb_anhydrase	ECOD (develop294)
L [auth M]	Oxidored_q6	e5aa5M1	A: alpha bundles	X: ACP-like	H: Acyl-carrier protein (ACP)	T: Acyl-carrier protein (ACP)	F: Oxidored_q6	ECOD (develop294)
H	Oxidored_q6	e5aa5H1	A: alpha bundles	X: ACP-like	H: Acyl-carrier protein (ACP)	T: Acyl-carrier protein (ACP)	F: Oxidored_q6	ECOD (develop294)
F	Glyco_hydro_31_2nd	e5aa5F1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F: Glyco_hydro_31_2nd	ECOD (develop294)
D	Glyco_hydro_31_2nd	e5aa5D1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F: Glyco_hydro_31_2nd	ECOD (develop294)
B	Oxidored_q6	e5aa5B1	A: alpha bundles	X: ACP-like	H: Acyl-carrier protein (ACP)	T: Acyl-carrier protein (ACP)	F: Oxidored_q6	ECOD (develop294)
A	Oxidored_q6	e5aa5A1	A: alpha bundles	X: ACP-like	H: Acyl-carrier protein (ACP)	T: Acyl-carrier protein (ACP)	F: Oxidored_q6	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
K [auth L]	1.10.645.10	Mainly Alpha	Orthogonal Bundle	Cytochrome-c3 Hydrogenase	chain B	CATH (4.3.0)
J [auth K]	1.10.645.10	Mainly Alpha	Orthogonal Bundle	Cytochrome-c3 Hydrogenase	chain B	CATH (4.3.0)
I	1.10.645.10	Mainly Alpha	Orthogonal Bundle	Cytochrome-c3 Hydrogenase	chain B	CATH (4.3.0)
G	1.10.645.10	Mainly Alpha	Orthogonal Bundle	Cytochrome-c3 Hydrogenase	chain B	CATH (4.3.0)
E	1.10.645.10	Mainly Alpha	Orthogonal Bundle	Cytochrome-c3 Hydrogenase	chain B	CATH (4.3.0)
C	1.10.645.10	Mainly Alpha	Orthogonal Bundle	Cytochrome-c3 Hydrogenase	chain B	CATH (4.3.0)
L [auth M]	4.10.480.10	Few Secondary Structures	Irregular	Cytochrome-c3 Hydrogenase	Chain A, domain 2	CATH (4.3.0)
H	4.10.480.10	Few Secondary Structures	Irregular	Cytochrome-c3 Hydrogenase	Chain A, domain 2	CATH (4.3.0)
F	4.10.480.10	Few Secondary Structures	Irregular	Cytochrome-c3 Hydrogenase	Chain A, domain 2	CATH (4.3.0)
D	4.10.480.10	Few Secondary Structures	Irregular	Cytochrome-c3 Hydrogenase	Chain A, domain 2	CATH (4.3.0)
B	4.10.480.10	Few Secondary Structures	Irregular	Cytochrome-c3 Hydrogenase	Chain A, domain 2	CATH (4.3.0)
A	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
C, E, G, I, J [auth K], C, E, G, I, J [auth K], K [auth L]	PF00374	Nickel-dependent hydrogenase (NiFeSe_Hases)	Nickel-dependent hydrogenase	-	Family
A, B, D, F, H, A, B, D, F, H, L [auth M]	PF14720	NiFe/NiFeSe hydrogenase small subunit C-terminal (NiFe_hyd_SSU_C)	NiFe/NiFeSe hydrogenase small subunit C-terminal	-	Family
A, B, D, F, H, A, B, D, F, H, L [auth M]	PF01058	NADH ubiquinone oxidoreductase, 20 Kd subunit (Oxidored_q6)	NADH ubiquinone oxidoreductase, 20 Kd subunit		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, E, G, I, J [auth K], C, E, G, I, J [auth K], K [auth L]	NIFE-HYDROGENASE LARGE SUBUNIT, HOFG	cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding	-	-
A, B, D, F, H, A, B, D, F, H, L [auth M]	NIFE-HYDROGENASE SMALL SUBUNIT, HOFK	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	cellular anatomical structure membrane protein-containing complex catalytic complex oxidoreductase complex ferredoxin hydrogenase complex intracellular protein-containing complex [Ni-Fe] hydrogenase complex cell envelope

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, E, G, I, J [auth K], C, E, G, I, J [auth K], K [auth L]	IPR001501	Nickel-dependent hydrogenase, large subunit	Family
C, E, G, I, J [auth K], C, E, G, I, J [auth K], K [auth L]	IPR029014	[NiFe]-hydrogenase, large subunit	Homologous Superfamily
C, E, G, I, J [auth K], C, E, G, I, J [auth K], K [auth L]	IPR050867	[NiFe]/[NiFeSe] hydrogenase large subunit	Family
A, B, D, F, H, A, B, D, F, H, L [auth M]	IPR001821	[NiFe]-hydrogenase, small subunit	Family
A, B, D, F, H, A, B, D, F, H, L [auth M]	IPR027394	Cytochrome-c3 hydrogenase, C-terminal	Domain
A, B, D, F, H, A, B, D, F, H, L [auth M]	IPR006137	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	Domain
A, B, D, F, H, A, B, D, F, H, L [auth M]	IPR037024	[NiFe]-hydrogenase, small subunit, N-terminal domain superfamily	Homologous Superfamily
A, B, D, F, H, A, B, D, F, H, L [auth M]	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.