7T2R | pdb_00007t2r

Structure of electron bifurcating Ni-Fe hydrogenase complex HydABCSL in FMN-free apo state

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
I	SCOP2B Superfamily	HydB/Nqo4-like	8106924	3001849	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	HydB/Nqo4-like	8106924	3001849	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Thioredoxin-like	8106926	3000031	SCOP2B (2022-06-29)
C	SCOP2 Family	NQO2-like	8106925	4002945	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Thioredoxin-like	8106926	3000031	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
J	SBP_bac_11	e7t2rJ1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: SBP_bac_11	ECOD (v294.1)
E	Fer2_4	e7t2rE1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Fer2_4	ECOD (v294.1)
I	SBP_bac_11	e7t2rI1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: SBP_bac_11	ECOD (v294.1)
D	Fer2_4	e7t2rD1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Fer2_4	ECOD (v294.1)
H	SBP_bac_11	e7t2rH1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: SBP_bac_11	ECOD (v294.1)
C	Fer2_4	e7t2rC1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Fer2_4	ECOD (v294.1)
G	SBP_bac_11	e7t2rG1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: SBP_bac_11	ECOD (v294.1)
B	Fer2_4	e7t2rB1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Fer2_4	ECOD (v294.1)
F	SBP_bac_11	e7t2rF1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: SBP_bac_11	ECOD (v294.1)
A	SBP_bac_11	e7t2rA1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: SBP_bac_11	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	1.10.10.1590	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	NADH-quinone oxidoreductase subunit E	CATH (utative)
H	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (utative)
C	1.10.10.1590	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	NADH-quinone oxidoreductase subunit E	CATH (utative)
C	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E, J	PF01058	NADH ubiquinone oxidoreductase, 20 Kd subunit (Oxidored_q6)	NADH ubiquinone oxidoreductase, 20 Kd subunit		Domain
D, I	PF00374	Nickel-dependent hydrogenase (NiFeSe_Hases)	Nickel-dependent hydrogenase	-	Family
C, H	PF01257	Thioredoxin-like [2Fe-2S] ferredoxin (2Fe-2S_thioredx)	Thioredoxin-like [2Fe-2S] ferredoxin	-	Family
B, G	PF10531	SLBB domain (SLBB)	SLBB domain		Domain
B, G	PF01512	Nuo51 FMN-binding domain (Complex1_51K)	Nuo51 FMN-binding domain	This entry represents the FMN-binding domain of NADH-ubiquinone oxidoreductase 51kDa subunit from NADH:ubiquinone oxidoreductase.	Domain
B, G	PF10589	NADH-ubiquinone oxidoreductase-F iron-sulfur binding region (NADH_4Fe-4S)	NADH-ubiquinone oxidoreductase-F iron-sulfur binding region		Domain
A, F	PF04879	Molybdopterin oxidoreductase Fe4S4 domain (Molybdop_Fe4S4)	Molybdopterin oxidoreductase Fe4S4 domain	This domain is found in formate dehydrogenase H for which the structure is known. This first domain (residues 1 to 60) of PDB:1aa6 is an Fe4S4 cluster just below the protein surface [1].	Domain
A, F	PF00384	Molybdopterin oxidoreductase (Molybdopterin)	Molybdopterin oxidoreductase		Domain
A, F	PF22117	NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain (Fer4_Nqo3)	NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain	NADH-quinone oxidoreductase subunit 3 (Nqo3) is a component of respiratory complex I. This protein is located at the peripheral arm of the complex and consists of multiple domains. This entry represents the second ferredoxin-like domain which contain ...	NADH-quinone oxidoreductase subunit 3 (Nqo3) is a component of respiratory complex I. This protein is located at the peripheral arm of the complex and consists of multiple domains. This entry represents the second ferredoxin-like domain which contains Fe4-S4 cluster, one of the redox centers of the complex [1-5].	Domain
A, F	PF13510	2Fe-2S iron-sulfur cluster binding domain (Fer2_4)	2Fe-2S iron-sulfur cluster binding domain	The 2Fe-2S ferredoxin family have a general core structure consisting of beta(2)-alpha-beta(2) which a beta-grasp type fold. The domain is around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated. Th ...	The 2Fe-2S ferredoxin family have a general core structure consisting of beta(2)-alpha-beta(2) which a beta-grasp type fold. The domain is around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated. This cluster appears within sarcosine oxidase proteins.	Domain
A, F	PF10588	NADH-ubiquinone oxidoreductase-G iron-sulfur binding region (NADH-G_4Fe-4S_3)	NADH-ubiquinone oxidoreductase-G iron-sulfur binding region		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, J	NiFe hydrogenase small subunit	oxidoreductase activity catalytic activity iron-sulfur cluster binding binding metal cluster binding small molecule binding	-	-
D, I	NiFe 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	-	-
C, H	NiFe hydrogenase subunit C	oxidoreductase activity catalytic activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	-	-
B, G	NiFe hydrogenase subunit B	FMN binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity electron transfer activity FMN binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity electron transfer activity active monoatomic ion transmembrane transporter activity NADH dehydrogenase (ubiquinone) activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding cation binding metal ion binding	-	-
A, F	NiFe hydrogenase subunit A	iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on NAD(P)H catalytic activity NADH dehydrogenase activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity electron transfer activity active monoatomic ion transmembrane transporter activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on NAD(P)H catalytic activity NADH dehydrogenase activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity electron transfer activity active monoatomic ion transmembrane transporter activity NADH dehydrogenase (ubiquinone) activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity quinone binding 4 iron, 4 sulfur cluster binding cation binding ion binding metal ion binding	aerobic respiration cellular respiration oxidative phosphorylation energy derivation by oxidation of organic compounds respiratory electron transport chain ATP synthesis coupled electron transport electron transport chain metabolic process cellular process generation of precursor metabolites and energy	cellular anatomical structure membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E, J	IPR051349	Hydrogenase complex-associated protein	Family
E, J	IPR037024	[NiFe]-hydrogenase, small subunit, N-terminal domain superfamily	Homologous Superfamily
E, J	IPR006137	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	Domain
D, I	IPR001501	Nickel-dependent hydrogenase, large subunit	Family
D, I	IPR029014	[NiFe]-hydrogenase, large subunit	Homologous Superfamily
D, I	IPR018194	Nickel-dependent hydrogenase, large subunit, nickel binding site	Binding Site
C, H	IPR028431	NADP-reducing hydrogenase subunit HndA-like	Family
C, H	IPR042128	NuoE domain	Domain
C, H	IPR002023	NADH-quinone oxidoreductase subunit E-like	Family
C, H	IPR041921	NADH-quinone oxidoreductase subunit E, N-terminal	Homologous Superfamily
C, H	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily
B, G	IPR019575	NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain	Domain
B, G	IPR019554	Soluble ligand binding domain	Domain
B, G	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
B, G	IPR001949	NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site	Conserved Site
B, G	IPR037225	NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily	Homologous Superfamily
B, G	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
B, G	IPR037207	NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily	Homologous Superfamily
B, G	IPR011538	NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain	Domain
B, G	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily
A, F	IPR006963	Molybdopterin oxidoreductase, 4Fe-4S domain	Domain
A, F	IPR006656	Molybdopterin oxidoreductase	Domain
A, F	IPR036010	2Fe-2S ferredoxin-like superfamily	Homologous Superfamily
A, F	IPR001041	2Fe-2S ferredoxin-type iron-sulfur binding domain	Domain
A, F	IPR000283	NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site	Conserved Site
A, F	IPR054351	NADH-ubiquinone oxidoreductase, ferredoxin-like domain	Domain
A, F	IPR050123	Prok_molybdopt-oxidoreductase	Unknown
A, F	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
A, F	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
A, F	IPR019574	NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding	Domain