8BXX

Crystal structure of formate dehydrogenase FDH2 enzyme from Granulicella mallensis MP5ACTX8 in complex with NAD and azide.

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
A [auth AA]	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8097858	3000044	SCOP2B (2022-06-29)
C [auth CC]	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8097858	3000044	SCOP2B (2022-06-29)
D [auth DD]	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8097858	3000044	SCOP2B (2022-06-29)
B [auth BB]	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8097858	3000044	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 [auth AA]	PF02826	e8bxxAA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: PF02826	ECOD (1.6)
A [auth AA]	PF00389	e8bxxAA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Formate/glycerate dehydrogenase catalytic domain-like	F: PF00389	ECOD (1.6)
C [auth CC]	PF02826	e8bxxCC2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: PF02826	ECOD (1.6)
C [auth CC]	PF00389	e8bxxCC1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Formate/glycerate dehydrogenase catalytic domain-like	F: PF00389	ECOD (1.6)
D [auth DD]	PF02826	e8bxxDD2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: PF02826	ECOD (1.6)
D [auth DD]	PF00389	e8bxxDD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Formate/glycerate dehydrogenase catalytic domain-like	F: PF00389	ECOD (1.6)
B [auth BB]	PF02826	e8bxxBB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: PF02826	ECOD (1.6)
B [auth BB]	PF00389	e8bxxBB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Formate/glycerate dehydrogenase catalytic domain-like	F: PF00389	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth AA], B [auth BB], C [auth CC], D [auth DD]	PF02826	D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain (2-Hacid_dh_C)	D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain	This domain is inserted into the catalytic domain, the large dehydrogenase and D-lactate dehydrogenase families in SCOP. N-terminal portion of which is represented by family Pfam:PF00389.	Domain
A [auth AA], B [auth BB], C [auth CC], D [auth DD]	PF00389	D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain (2-Hacid_dh)	D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain	This family represents the largest portion of the catalytic domain of 2-hydroxyacid dehydrogenases as the NAD binding domain is inserted within the structural domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth AA], B [auth BB], C [auth CC], D [auth DD]	Formate dehydrogenase	oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors catalytic activity NAD binding binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding small molecule binding formate dehydrogenase (NAD+) activity oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors catalytic activity NAD binding binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding adenyl nucleotide binding nucleotide binding heterocyclic compound 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	catabolic process oxoacid metabolic process cellular metabolic process carboxylic acid metabolic process organic acid metabolic process organic acid catabolic process formate catabolic process cellular catabolic process organic substance metabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process small molecule metabolic process metabolic process cellular process catabolic process oxoacid metabolic process cellular metabolic process carboxylic acid metabolic process organic acid metabolic process organic acid catabolic process formate catabolic process cellular catabolic process organic substance metabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process small molecule metabolic process metabolic process cellular process monocarboxylic acid metabolic process small molecule catabolic process formate metabolic process organic substance catabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth AA], B [auth BB], C [auth CC], D [auth DD]	IPR033689	NAD-dependent formate dehydrogenase	Family
A [auth AA], B [auth BB], C [auth CC], D [auth DD]	IPR006139	D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain	Domain
A [auth AA], B [auth BB], C [auth CC], D [auth DD]	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A [auth AA], B [auth BB], C [auth CC], D [auth DD]	IPR029752	D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1	Conserved Site
A [auth AA], B [auth BB], C [auth CC], D [auth DD]	IPR029753	D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site	Conserved Site
A [auth AA], B [auth BB], C [auth CC], D [auth DD]	IPR006140	D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain	Domain

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 R01GM133198.