4GD3 | pdb_00004gd3

Structure of E. coli hydrogenase-1 in complex with cytochrome b

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
J [auth B]	POC3_POC4	e4gd3B2	A: alpha arrays	X: Fusion glycoprotein F2	H: Fusion glycoprotein F2	T: Fusion glycoprotein F2	F: POC3_POC4	ECOD (v295.2)
I [auth A]	Peptidase_M4,Peptidase_M4_C	e4gd3A1	A: alpha arrays	X: GIY-YIG endonuclease	H: GIY-YIG endonuclease	T: GIY-YIG endonuclease	F: Peptidase_M4,Peptidase_M4_C	ECOD (v295.2)
H [auth K]	Glyco_hydro_70	e4gd3K1	A: alpha arrays	X: Lipocalins/Streptavidin	H: SAM/DNA-glycosylase	T: SAM domain-like	F: Glyco_hydro_70	ECOD (v295.2)
F [auth J]	Glyco_hydro_70	e4gd3J1	A: alpha arrays	X: Lipocalins/Streptavidin	H: SAM/DNA-glycosylase	T: SAM domain-like	F: Glyco_hydro_70	ECOD (v295.2)
D [auth M]	Glyco_hydro_70	e4gd3M1	A: alpha arrays	X: Lipocalins/Streptavidin	H: SAM/DNA-glycosylase	T: SAM domain-like	F: Glyco_hydro_70	ECOD (v295.2)
B [auth L]	Endonuclease_NS	e4gd3L1	A: alpha arrays	X: Lipocalins/Streptavidin	H: SAM/DNA-glycosylase	T: SAM domain-like	F: Endonuclease_NS	ECOD (v295.2)
G [auth R]	V-set	e4gd3R1	A: alpha arrays	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: V-set	ECOD (v295.2)
G [auth R]	HMGL-like	e4gd3R3	A: alpha arrays	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: HMGL-like	ECOD (v295.2)
E [auth Q]	V-set	e4gd3Q1	A: alpha arrays	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: V-set	ECOD (v295.2)
E [auth Q]	HMGL-like	e4gd3Q3	A: alpha arrays	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: HMGL-like	ECOD (v295.2)
C [auth T]	V-set	e4gd3T1	A: alpha arrays	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: V-set	ECOD (v295.2)
C [auth T]	HMGL-like	e4gd3T3	A: alpha arrays	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: HMGL-like	ECOD (v295.2)
A [auth S]		e4gd3S1	A: alpha arrays	X: Macro domain-like	H: Macro domain-like	T: Macro domain-like	F:	ECOD (v295.2)
A [auth S]	ABC_tran	e4gd3S2	A: alpha arrays	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F: ABC_tran	ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
J [auth B]	1.20.950.20	Mainly Alpha	Up-down Bundle	Fumarate Reductase Cytochrome B subunit	Transmembrane di-heme cytochromes, Chain C	CATH (4.3.0)
I [auth A]	1.20.950.20	Mainly Alpha	Up-down Bundle	Fumarate Reductase Cytochrome B subunit	Transmembrane di-heme cytochromes, Chain C	CATH (4.3.0)
H [auth K]	1.10.645.10	Mainly Alpha	Orthogonal Bundle	Cytochrome-c3 Hydrogenase	chain B	CATH (4.3.0)
F [auth J]	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)
B [auth L]	1.10.645.10	Mainly Alpha	Orthogonal Bundle	Cytochrome-c3 Hydrogenase	chain B	CATH (4.3.0)
G [auth R]	3.40.50.700	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	CATH (4.3.0)
G [auth R]	4.10.480.10	Few Secondary Structures	Irregular	Cytochrome-c3 Hydrogenase	Chain A, domain 2	CATH (4.3.0)
E [auth Q]	3.40.50.700	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	CATH (4.3.0)
E [auth Q]	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)
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
I [auth A], J [auth B]	PF01292	Prokaryotic cytochrome b561 (Ni_hydr_CYTB)	Prokaryotic cytochrome b561	This family includes cytochrome b561 and related proteins, in addition to the nickel-dependent hydrogenases b-type cytochrome subunit. Cytochrome b561 is a secretory vesicle-specific electron transport protein. It is an integral membrane protein, th ...	This family includes cytochrome b561 and related proteins, in addition to the nickel-dependent hydrogenases b-type cytochrome subunit. Cytochrome b561 is a secretory vesicle-specific electron transport protein. It is an integral membrane protein, that binds two heme groups non-covalently. This is a prokaryotic family. Members of the 'eukaryotic cytochrome b561' family can be found in Pfam: PF03188.	Domain
B [auth L], D [auth M], F [auth J], H [auth K]	PF00374	Nickel-dependent hydrogenase (NiFeSe_Hases)	Nickel-dependent hydrogenase	-	Family
A [auth S], C [auth T], E [auth Q], G [auth R]	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], E [auth Q], G [auth R]	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
I [auth A], J [auth B]	Ni/Fe-hydrogenase 1 B-type cytochrome subunit	binding tetrapyrrole binding heme binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding hydrogenase (acceptor) activity oxidoreductase activity oxidoreductase activity, acting on hydrogen as donor catalytic activity electron transfer activity	cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress cellular process response to starvation cellular response to starvation anaerobic electron transport chain cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress cellular process response to starvation cellular response to starvation anaerobic electron transport chain cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain metabolic process generation of precursor metabolites and energy anaerobic respiration hydrogen metabolic process	protein-containing complex catalytic complex [Ni-Fe] hydrogenase complex cell periphery cellular anatomical structure plasma membrane membrane cell surface periplasmic side of plasma membrane external side of plasma membrane side of membrane
B [auth L], D [auth M], F [auth J], H [auth K]	Hydrogenase-1 large chain	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 hydrogenase (acceptor) activity electron transfer activity	cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress cellular process response to starvation cellular response to starvation anaerobic electron transport chain cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress cellular process response to starvation cellular response to starvation anaerobic electron transport chain cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain metabolic process generation of precursor metabolites and energy anaerobic respiration hydrogen metabolic process	cellular anatomical structure membrane protein-containing complex catalytic complex [Ni-Fe] hydrogenase complex cell periphery cell surface periplasmic side of plasma membrane plasma membrane external side of plasma membrane side of membrane extracellular region outer membrane-bounded periplasmic space cell envelope cellular anatomical structure membrane protein-containing complex catalytic complex [Ni-Fe] hydrogenase complex cell periphery cell surface periplasmic side of plasma membrane plasma membrane external side of plasma membrane side of membrane extracellular region outer membrane-bounded periplasmic space cell envelope periplasmic space
A [auth S], C [auth T], E [auth Q], G [auth R]	Hydrogenase-1 small chain	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 response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress cellular process response to starvation cellular response to starvation anaerobic electron transport chain cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress cellular process response to starvation cellular response to starvation anaerobic electron transport chain cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain metabolic process generation of precursor metabolites and energy anaerobic respiration hydrogen metabolic process	cellular anatomical structure membrane protein-containing complex catalytic complex oxidoreductase complex ferredoxin hydrogenase complex intracellular protein-containing complex [Ni-Fe] hydrogenase complex cell periphery cell surface periplasmic side of plasma membrane plasma membrane external side of plasma membrane side of membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I [auth A], J [auth B]	IPR051542	Hydrogenase-associated cytochrome	Family
I [auth A], J [auth B]	IPR011577	Cytochrome b561, bacterial/Ni-hydrogenase	Domain
I [auth A], J [auth B]	IPR016174	Di-haem cytochrome, transmembrane	Homologous Superfamily
I [auth A], J [auth B]	IPR000516	Nickel-dependent hydrogenase b-type cytochrome subunit	Family
B [auth L], D [auth M], F [auth J], H [auth K]	IPR001501	Nickel-dependent hydrogenase, large subunit	Family
B [auth L], D [auth M], F [auth J], H [auth K]	IPR029014	[NiFe]-hydrogenase, large subunit	Homologous Superfamily
B [auth L], D [auth M], F [auth J], H [auth K]	IPR050867	[NiFe]/[NiFeSe] hydrogenase large subunit	Family
B [auth L], D [auth M], F [auth J], H [auth K]	IPR018194	Nickel-dependent hydrogenase, large subunit, nickel binding site	Binding Site
A [auth S], C [auth T], E [auth Q], G [auth R]	IPR006311	Twin-arginine translocation pathway, signal sequence	Conserved Site
A [auth S], C [auth T], E [auth Q], G [auth R]	IPR001821	[NiFe]-hydrogenase, small subunit	Family
A [auth S], C [auth T], E [auth Q], G [auth R]	IPR027394	Cytochrome-c3 hydrogenase, C-terminal	Domain
A [auth S], C [auth T], E [auth Q], G [auth R]	IPR006137	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	Domain
A [auth S], C [auth T], E [auth Q], G [auth R]	IPR037024	[NiFe]-hydrogenase, small subunit, N-terminal domain superfamily	Homologous Superfamily
A [auth S], C [auth T], E [auth Q], G [auth R]	IPR019546	Twin-arginine translocation pathway, signal sequence, bacterial/archaeal	Conserved Site
A [auth S], C [auth T], E [auth Q], G [auth R]	IPR037148	[NiFe]-hydrogenase, small subunit, C-terminal domain superfamily	Homologous Superfamily

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A [auth S], B [auth L], C [auth T], D [auth M], E [auth Q] A [auth S], B [auth L], C [auth T], D [auth M], E [auth Q], F [auth J], G [auth R], H [auth K], I [auth A], J [auth B]	OPM	Transmembrane	Alpha-helical polytopic	Electron transport chain complex III (bc1 and b6f) superfamily	Prokaryotic cytochrome b561

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A [auth S], B [auth L], C [auth T], D [auth M], E [auth Q] A [auth S], B [auth L], C [auth T], D [auth M], E [auth Q], F [auth J], G [auth R], H [auth K], I [auth A], J [auth B]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A [auth S], B [auth L], C [auth T], D [auth M], E [auth Q] A [auth S], B [auth L], C [auth T], D [auth M], E [auth Q], F [auth J], G [auth R], H [auth K], I [auth A], J [auth B]	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A [auth S], B [auth L], C [auth T], D [auth M], E [auth Q] A [auth S], B [auth L], C [auth T], D [auth M], E [auth Q], F [auth J], G [auth R], H [auth K], I [auth A], J [auth B]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Oxidoreductases	O₂-tolerant Hydrogenase-1 in complex with cytochrome b

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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.