5ODR

Heterodisulfide reductase / [NiFe]-hydrogenase complex from Methanothermococcus thermolithotrophicus soaked with heterodisulfide for 2 minutes.

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
F	d5odrf_	Multi-domain proteins (alpha and beta)	HydB/Nqo4-like	HydB/Nqo4-like	automated matches	automated matches	(Methanothermococcus thermolithotrophicus DSM 2095 ) [TaxId: 523845 ],	SCOPe (2.08)
L	d5odrl_	Multi-domain proteins (alpha and beta)	HydB/Nqo4-like	HydB/Nqo4-like	automated matches	automated matches	(Methanothermococcus thermolithotrophicus DSM 2095 ) [TaxId: 523845 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	HydB/Nqo4-like	8096642	3001849	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	HydB/Nqo4-like	8096642	3001849	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	Fer4_21_1	e5odrA3	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Fer4_21_1	ECOD (1.6)
A	FAD_binding_3_1st	e5odrA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: FAD_binding_3_1st	ECOD (1.6)
A	Pyr_redox_2	e5odrA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Pyr_redox_2	ECOD (1.6)
G	Fer4_21_1	e5odrG3	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Fer4_21_1	ECOD (1.6)
G	FAD_binding_3_1st	e5odrG1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: FAD_binding_3_1st	ECOD (1.6)
G	Pyr_redox_2	e5odrG2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Pyr_redox_2	ECOD (1.6)
B	CoB_CoM_SS_B_like	e5odrB1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: ATC-like	F: CoB_CoM_SS_B_like	ECOD (1.6)
B	UNK_F_TYPE	e5odrB2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: ATC-like	F: UNK_F_TYPE	ECOD (1.6)
H	CoB_CoM_SS_B_like	e5odrH2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: ATC-like	F: CoB_CoM_SS_B_like	ECOD (1.6)
H	UNK_F_TYPE	e5odrH1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: ATC-like	F: UNK_F_TYPE	ECOD (1.6)
I	Fer4_8	e5odrI1	A: alpha arrays	X: alpha-helical ferredoxin-like	H: alpha-helical ferredoxin (From Topology)	T: alpha-helical ferredoxin	F: Fer4_8	ECOD (1.6)
C	Fer4_8	e5odrC1	A: alpha arrays	X: alpha-helical ferredoxin-like	H: alpha-helical ferredoxin (From Topology)	T: alpha-helical ferredoxin	F: Fer4_8	ECOD (1.6)
D	UNK_F_TYPE	e5odrD1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Methyl-viologen reducing hydrogenase subunit D (From Topology)	T: Methyl-viologen reducing hydrogenase subunit D	F: UNK_F_TYPE	ECOD (1.6)
J	UNK_F_TYPE	e5odrJ1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Methyl-viologen reducing hydrogenase subunit D (From Topology)	T: Methyl-viologen reducing hydrogenase subunit D	F: UNK_F_TYPE	ECOD (1.6)
E	Oxidored_q6	e5odrE2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Oxidored_q6	ECOD (1.6)
E	UNK_F_TYPE	e5odrE1	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: UNK_F_TYPE	ECOD (1.6)
K	Oxidored_q6	e5odrK1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Oxidored_q6	ECOD (1.6)
K	UNK_F_TYPE	e5odrK2	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: UNK_F_TYPE	ECOD (1.6)
F	NiFeSe_Hases_1st	e5odrF4	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)
F	NiFeSe_Hases_3rd	e5odrF3	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)
F	NiFeSe_Hases_3rd_1	e5odrF2	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)
L	NiFeSe_Hases_1st	e5odrL4	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)
L	NiFeSe_Hases_3rd	e5odrL3	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)
L	NiFeSe_Hases_3rd_1	e5odrL1	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, G	PF13187	4Fe-4S dicluster domain (Fer4_9)	4Fe-4S dicluster domain	-	Family
A, G	PF00890	FAD binding domain (FAD_binding_2)	FAD binding domain	-	Family
A, G	PF12838	4Fe-4S dicluster domain (Fer4_7)	4Fe-4S dicluster domain	Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contai ...	Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters.	Domain
B, H	PF02754	Cysteine-rich domain (CCG)	Cysteine-rich domain	-	Family
C, I	PF13183	4Fe-4S dicluster domain (Fer4_8)	4Fe-4S dicluster domain	Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contai ...	Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters.	Domain
D, J	PF02662	Methyl-viologen-reducing hydrogenase, delta subunit (FlpD)	Methyl-viologen-reducing hydrogenase, delta subunit	-	Family
E, K	PF01058	NADH ubiquinone oxidoreductase, 20 Kd subunit (Oxidored_q6)	NADH ubiquinone oxidoreductase, 20 Kd subunit	-	Family
F, L	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, G	Heterodisulfide reductase, subunit A	oxidoreductase activity catalytic activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding cation binding ion binding metal ion binding	-	-
B, H	Heterodisulfide reductase, subunit B	oxidoreductase activity, acting on a sulfur group of donors CoB--CoM heterodisulfide reductase activity oxidoreductase activity catalytic activity	cellular respiration energy derivation by oxidation of organic compounds cellular biosynthetic process cellular metabolic process alkane biosynthetic process methane metabolic process generation of precursor metabolites and energy hydrocarbon metabolic process biosynthetic process energy derivation by oxidation of reduced inorganic compounds cellular alkane metabolic process methanogenesis metabolic process cellular process cellular respiration energy derivation by oxidation of organic compounds cellular biosynthetic process cellular metabolic process alkane biosynthetic process methane metabolic process generation of precursor metabolites and energy hydrocarbon metabolic process biosynthetic process energy derivation by oxidation of reduced inorganic compounds cellular alkane metabolic process methanogenesis metabolic process cellular process hydrocarbon biosynthetic process anaerobic respiration	-
C, I	Heterodisulfide reductase, subunit C	oxidoreductase activity, acting on a sulfur group of donors CoB--CoM heterodisulfide reductase activity oxidoreductase activity catalytic 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	cellular respiration energy derivation by oxidation of organic compounds cellular biosynthetic process cellular metabolic process alkane biosynthetic process methane metabolic process generation of precursor metabolites and energy hydrocarbon metabolic process biosynthetic process energy derivation by oxidation of reduced inorganic compounds cellular alkane metabolic process methanogenesis metabolic process cellular process cellular respiration energy derivation by oxidation of organic compounds cellular biosynthetic process cellular metabolic process alkane biosynthetic process methane metabolic process generation of precursor metabolites and energy hydrocarbon metabolic process biosynthetic process energy derivation by oxidation of reduced inorganic compounds cellular alkane metabolic process methanogenesis metabolic process cellular process hydrocarbon biosynthetic process anaerobic respiration	-
D, J	Methyl-viologen reducing hydrogenase, subunit D	oxidoreductase activity, acting on a sulfur group of donors CoB--CoM heterodisulfide reductase activity 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	-	-
E, K	Methyl-viologen reducing hydrogenase, subunit G	hydrogenase (acceptor) activity oxidoreductase activity oxidoreductase activity, acting on hydrogen as donor catalytic activity hydrogen dehydrogenase activity oxidoreductase activity, acting on hydrogen as donor, NAD or NADP as acceptor iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	-	-
F, L	Methyl-viologen reducing hydrogenase, subunit A	hydrogenase (acceptor) activity oxidoreductase activity oxidoreductase activity, acting on hydrogen as donor catalytic activity cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding oxidoreductase activity, acting on hydrogen as donor, iron-sulfur protein as acceptor ferredoxin hydrogenase activity hydrogen dehydrogenase activity hydrogenase (acceptor) activity oxidoreductase activity oxidoreductase activity, acting on hydrogen as donor catalytic activity cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding oxidoreductase activity, acting on hydrogen as donor, iron-sulfur protein as acceptor ferredoxin hydrogenase activity hydrogen dehydrogenase activity oxidoreductase activity, acting on hydrogen as donor, NAD or NADP as acceptor	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, G	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
A, G	IPR039650	H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like	Family
A, G	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
A, G	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A, G	IPR003953	FAD-dependent oxidoreductase 2, FAD binding domain	Domain
B, H	IPR004017	Cysteine-rich domain	Domain
B, H	IPR017678	CoB--CoM heterodisulphide reductase, subunit B	Family
B, H	IPR051278	CoM-S-S-CoB heterodisulfide reductase	Family
C, I	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
C, I	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
C, I	IPR051460	Heterodisulfide reductase iron-sulfur subunit C	Family
C, I	IPR017680	CoB--CoM heterodisulphide reductase, subunit C	Family
C, I	IPR009051	Alpha-helical ferredoxin	Homologous Superfamily
D, J	IPR003813	F420-non-reducing hydrogenase iron-sulfur subunit D	Domain
E, K	IPR051349	Hydrogenase complex-associated protein	Family
E, K	IPR037024	[NiFe]-hydrogenase, small subunit, N-terminal domain superfamily	Homologous Superfamily
E, K	IPR006137	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	Domain
F, L	IPR001501	Nickel-dependent hydrogenase, large subunit	Family
F, L	IPR029014	[NiFe]-hydrogenase, large subunit	Homologous Superfamily
F, L	IPR018194	Nickel-dependent hydrogenase, large subunit, nickel binding site	Binding Site

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5ODR

Heterodisulfide reductase / [NiFe]-hydrogenase complex from Methanothermococcus thermolithotrophicus soaked with heterodisulfide for 2 minutes.

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Domain Annotation: ECOD Classification ECOD Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage