6SDR | pdb_00006sdr

W-formate dehydrogenase from Desulfovibrio vulgaris - Oxidized form

External Resource: Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d6sdrb_	Alpha and beta proteins (a+b)	Ferredoxin-like	4Fe-4S ferredoxins	Ferredoxin domains from multidomain proteins	automated matches	(Nitratidesulfovibrio vulgaris str. Hildenborough ) [TaxId: 882 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	4Fe-4S ferredoxins	8094124	3000020	SCOP2B (2022-06-29)
A	SCOP2 Family	Formate dehydrogenase/DMSO reductase, domains 1-3	8099885	4000801	SCOP2 (2022-06-29)
A	SCOP2 Family	Formate dehydrogenase/DMSO reductase, C-terminal domain	8101089	4002360	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Formate dehydrogenase/DMSO reductase, domains 1-3	8099886	3001453	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	ADC-like	8101090	3001132	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)
B		e6sdrB1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: YscJ_FliF	F:	ECOD (20:10:01)
A		e6sdrA1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: YscJ_FliF	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.70.20	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (utative)
A	3.40.50.740	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)
A	3.40.228.10	Alpha Beta	3-Layer(aba) Sandwich	Dimethylsulfoxide Reductase	domain 2	CATH (utative)
A	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF13247	4Fe-4S dicluster domain (Fer4_11)	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
A	PF01568	Molydopterin dinucleotide binding domain (Molydop_binding)	Molydopterin dinucleotide binding domain	This domain is found in various molybdopterin - containing oxidoreductases and tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where the domain constitutes almost the entire s ...	This domain is found in various molybdopterin - containing oxidoreductases and tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where the domain constitutes almost the entire subunit. The formylmethanofuran dehydrogenase catalyses the first step in methane formation from CO2 in methanogenic archaea and has a molybdopterin dinucleotide cofactor [1]. This domain corresponds to the C-terminal domain IV in dimethyl sulfoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules [2].	Domain
A	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	PF00384	Molybdopterin oxidoreductase (Molybdopterin)	Molybdopterin oxidoreductase		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Formate dehydrogenase, beta subunit, putative	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 anatomical structure cell envelope
A	Formate dehydrogenase, alpha subunit, selenocysteine-containing	cation binding transition metal ion binding molybdenum ion binding ion binding binding metal ion binding small molecule binding molybdopterin cofactor binding oxidoreductase activity, acting on the aldehyde or oxo group of donors, cytochrome as acceptor formate dehydrogenase (cytochrome-c-553) activity oxidoreductase activity oxidoreductase activity, acting on the aldehyde or oxo group of donors catalytic activity iron-sulfur cluster binding cation binding transition metal ion binding molybdenum ion binding ion binding binding metal ion binding small molecule binding molybdopterin cofactor binding oxidoreductase activity, acting on the aldehyde or oxo group of donors, cytochrome as acceptor formate dehydrogenase (cytochrome-c-553) activity oxidoreductase activity oxidoreductase activity, acting on the aldehyde or oxo group of donors catalytic activity iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding formate dehydrogenase (NAD+) activity oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor electron transfer activity	cellular respiration energy derivation by oxidation of organic compounds metabolic process cellular process generation of precursor metabolites and energy anaerobic respiration	cellular anatomical structure periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR051555	Formate Dehydrogenase Electron Transfer Unit	Family
B	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
A	IPR006963	Molybdopterin oxidoreductase, 4Fe-4S domain	Domain
A	IPR006657	Molybdopterin dinucleotide-binding domain	Domain
A	IPR006656	Molybdopterin oxidoreductase	Domain
A	IPR006443	Formate dehydrogenase-N, alpha subunit	Family
A	IPR006311	Twin-arginine translocation pathway, signal sequence	Conserved Site
A	IPR009010	Aspartate decarboxylase-like domain superfamily	Homologous Superfamily
A	IPR006655	Molybdopterin oxidoreductase, prokaryotic, conserved site	Conserved Site
A	IPR027467	Molybdopterin oxidoreductase, molybdopterin cofactor binding site	Binding Site
A	IPR019546	Twin-arginine translocation pathway, signal sequence, bacterial/archaeal	Conserved Site

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.