7BKD | pdb_00007bkd

Formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex from Methanospirillum hungatei (heterodislfide reductase core and mobile arm in conformational state 1, composite structure)

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 [auth D]	SCOP2B Superfamily	Formate dehydrogenase/DMSO reductase, domains 1-3	8105473	3001453	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	e7bkdA4	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	e7bkdA2	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	e7bkdA1	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 [auth C]	Fer4_8	e7bkdC1	A: alpha arrays	X: alpha-helical ferredoxin-like	H: alpha-helical ferredoxin (From Topology)	T: alpha-helical ferredoxin	F: Fer4_8	ECOD (1.6)
E [auth c]	Fer4_8	e7bkdc1	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 [auth B]	F_UNCLASSIFIED	e7bkdB1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: ATC-like	F: F_UNCLASSIFIED	ECOD (1.6)
C [auth B]	CoB_CoM_SS_B_like	e7bkdB2	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)
F [auth b]	F_UNCLASSIFIED	e7bkdb2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: ATC-like	F: F_UNCLASSIFIED	ECOD (1.6)
F [auth b]	CoB_CoM_SS_B_like	e7bkdb1	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)
G [auth F]	F_UNCLASSIFIED	e7bkdF1	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: F_UNCLASSIFIED	ECOD (1.6)
I [auth D]	Molybdop_Fe4S4	e7bkdD3	A: a+b two layers	X: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)	H: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domain 1	F: Molybdop_Fe4S4	ECOD (1.6)
I [auth D]	Molybdopterin_2nd	e7bkdD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domains 2 and 3	F: Molybdopterin_2nd	ECOD (1.6)
I [auth D]	Molybdopterin_1st_1	e7bkdD2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domains 2 and 3	F: Molybdopterin_1st_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.70.20	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (utative)
B [auth C]	1.10.1060.10	Mainly Alpha	Orthogonal Bundle	Fumarate Reductase Iron-sulfur Protein	Chain B, domain 2	CATH (utative)
E [auth c]	1.10.1060.10	Mainly Alpha	Orthogonal Bundle	Fumarate Reductase Iron-sulfur Protein	Chain B, domain 2	CATH (utative)
C [auth B]	1.20.1050.140	Mainly Alpha	Up-down Bundle	Glutathione S-transferase Yfyf (Class Pi)	Chain A, domain 2	CATH (utative)
F [auth b]	1.20.1050.140	Mainly Alpha	Up-down Bundle	Glutathione S-transferase Yfyf (Class Pi)	Chain A, domain 2	CATH (utative)
I [auth D]	3.40.228.10	Alpha Beta	3-Layer(aba) Sandwich	Dimethylsulfoxide Reductase	domain 2	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D [auth a]	PF12831	FAD dependent oxidoreductase (FAD_oxidored)	FAD dependent oxidoreductase	-	Family
A, D [auth a]	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 [auth C], E [auth c]	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
C [auth B], F [auth b]	PF02754	Cysteine-rich domain (CCG)	Cysteine-rich domain	The key element of this domain is the CX31-38CCX33-34CXXC sequence motif normally found at the C-terminus in archaeal and bacterial Hdr-like proteins [2]. There may be one or two copies, and the motif is probably an iron-sulfur binding cluster. In so ...	The key element of this domain is the CX31-38CCX33-34CXXC sequence motif normally found at the C-terminus in archaeal and bacterial Hdr-like proteins [2]. There may be one or two copies, and the motif is probably an iron-sulfur binding cluster. In some instances one of the cysteines is replaced by an aspartate, and aspartate can in principle also function as a ligand of an iron-sulfur cluster [2]. The entry includes a subunit from heterodisulphide reductase and a subunit from glycolate oxidase (Swiss:P52074) [1] and glycerol-3-phosphate dehydrogenase.	Domain
G [auth F]	PF02662	Methyl-viologen-reducing hydrogenase, delta subunit (FlpD)	Methyl-viologen-reducing hydrogenase, delta subunit	-	Family
H [auth E]	PF04422	Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term (FrhB_FdhB_N)	Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term	-	Family
H [auth E]	PF04432	Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus (FrhB_FdhB_C)	Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus	Coenzyme F420 hydrogenase (EC:1.12.99.1) reduces the low-potential two-electron acceptor coenzyme F420. This family contains the C termini of F420 hydrogenase and dehydrogenase beta subunits [1], [2]. The N terminus of Methanobacterium formicicum fo ...	Coenzyme F420 hydrogenase (EC:1.12.99.1) reduces the low-potential two-electron acceptor coenzyme F420. This family contains the C termini of F420 hydrogenase and dehydrogenase beta subunits [1], [2]. The N terminus of Methanobacterium formicicum formate dehydrogenase beta chain (EC:1.2.1.2, Swiss:P06130) is also a member of this family [3]. This region is often found in association with the 4Fe-4S binding domain, fer4 (Pfam:PF00037).	Domain
I [auth D]	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
I [auth D]	PF00384	Molybdopterin oxidoreductase (Molybdopterin)	Molybdopterin oxidoreductase		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D [auth a]	CoB--CoM heterodisulfide reductase iron-sulfur subunit A	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	-	-
B [auth C], E [auth c]	CoB--CoM 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	cellular respiration energy derivation by oxidation of organic compounds 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 methanogenesis metabolic process cellular process hydrocarbon biosynthetic process anaerobic respiration	cell periphery cellular anatomical structure plasma membrane membrane
C [auth B], F [auth b]	CoB--CoM heterodisulfide reductase subunit B	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	cellular respiration energy derivation by oxidation of organic compounds 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 methanogenesis metabolic process cellular process hydrocarbon biosynthetic process anaerobic respiration	-
G [auth F]	F420-non-reducing hydrogenase subunit D	oxidoreductase activity catalytic activity iron-sulfur cluster binding binding metal cluster binding small molecule binding	-	-
H [auth E]	Formate dehydrogenase, beta subunit (F420)	iron-sulfur cluster binding binding metal cluster binding small molecule binding oxidoreductase activity, acting on CH or CH2 groups, with an iron-sulfur protein as acceptor oxidoreductase activity oxidoreductase activity, acting on CH or CH2 groups catalytic activity	-	-
I [auth D]	Formate dehydrogenase	oxidoreductase activity oxidoreductase activity, acting on NAD(P)H catalytic activity NADH dehydrogenase activity binding molybdopterin cofactor binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding formate dehydrogenase (NAD+) activity oxidoreductase activity, acting on the aldehyde or oxo group of donors oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor cation binding oxidoreductase activity oxidoreductase activity, acting on NAD(P)H catalytic activity NADH dehydrogenase activity binding molybdopterin cofactor binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding formate dehydrogenase (NAD+) activity oxidoreductase activity, acting on the aldehyde or oxo group of donors oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor cation binding ion binding metal ion binding	oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process metabolic process cellular process monocarboxylic acid metabolic process organic acid metabolic process formate metabolic process cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain generation of precursor metabolites and energy	cellular anatomical structure membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D [auth a]	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
A, D [auth a]	IPR039650	H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like	Family
A, D [auth a]	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
A, D [auth a]	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
B [auth C], E [auth c]	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
B [auth C], E [auth c]	IPR051460	HdrC_iron-sulfur_subunit	Unknown
B [auth C], E [auth c]	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
B [auth C], E [auth c]	IPR017680	CoB--CoM heterodisulphide reductase, subunit C	Family
B [auth C], E [auth c]	IPR009051	Alpha-helical ferredoxin	Homologous Superfamily
C [auth B], F [auth b]	IPR004017	Cysteine-rich domain	Domain
C [auth B], F [auth b]	IPR017678	CoB--CoM heterodisulphide reductase, subunit B	Family
C [auth B], F [auth b]	IPR051278	CoM-S-S-CoB heterodisulfide reductase	Family
G [auth F]	IPR003813	F420-non-reducing hydrogenase iron-sulfur subunit D	Domain
H [auth E]	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
H [auth E]	IPR045220	Oxidoreductase FRHB/FDHB/HCAR-like	Family
H [auth E]	IPR007516	Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal	Domain
H [auth E]	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
H [auth E]	IPR007525	Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal	Domain
I [auth D]	IPR006963	Molybdopterin oxidoreductase, 4Fe-4S domain	Domain
I [auth D]	IPR006657	Molybdopterin dinucleotide-binding domain	Domain
I [auth D]	IPR006656	Molybdopterin oxidoreductase	Domain
I [auth D]	IPR009010	Aspartate decarboxylase-like domain superfamily	Homologous Superfamily
I [auth D]	IPR006655	Molybdopterin oxidoreductase, prokaryotic, conserved site	Conserved Site
I [auth D]	IPR041924	Formate dehydrogenase H, N-terminal	Domain
I [auth D]	IPR050123	Prokaryotic molybdopterin-containing oxidoreductase	Family
I [auth D]	IPR027467	Molybdopterin oxidoreductase, molybdopterin cofactor binding site	Binding Site
I [auth D]	IPR006478	Formate dehydrogenase, alpha subunit	Family

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Formate dehydrogenase - heterodisulfide reductase - formylmethanofuran dehydrogenase complex from Methanospirillum hungatei (heterodislfide reductase core and mobile arm in conformational state 1, composite structure)

External Resource: Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Domain Annotation: ECOD Classification ECOD Database Homepage

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

7BKD | pdb_00007bkd