3N7U | pdb_00003n7u

NAD-dependent formate dehydrogenase from higher-plant Arabidopsis thaliana in complex with NAD and azide

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)
L	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8080189	3000044	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8080189	3000044	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8080189	3000044	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8080189	3000044	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8080189	3000044	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8080189	3000044	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8080189	3000044	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8080189	3000044	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8080189	3000044	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8080189	3000044	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8080189	3000044	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8080189	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)
L		e3n7uL1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Cytochrome_CBB3	F:	ECOD (20:10:01)
K		e3n7uK1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Cytochrome_CBB3	F:	ECOD (20:10:01)
J		e3n7uJ1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Cytochrome_CBB3	F:	ECOD (20:10:01)
I		e3n7uI1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Cytochrome_CBB3	F:	ECOD (20:10:01)
H		e3n7uH1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Cytochrome_CBB3	F:	ECOD (20:10:01)
G		e3n7uG1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Cytochrome_CBB3	F:	ECOD (20:10:01)
F		e3n7uF1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Cytochrome_CBB3	F:	ECOD (20:10:01)
E		e3n7uE1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Cytochrome_CBB3	F:	ECOD (20:10:01)
D		e3n7uD1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Cytochrome_CBB3	F:	ECOD (20:10:01)
C		e3n7uC1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Cytochrome_CBB3	F:	ECOD (20:10:01)
B		e3n7uB1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Cytochrome_CBB3	F:	ECOD (20:10:01)
A		e3n7uA1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Cytochrome_CBB3	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
K	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
J	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
I	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
H	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
G	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
F	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
E	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
D	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	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, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	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, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	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 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 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 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	response to stimulus response to stress response to wounding catabolic process oxoacid metabolic process carboxylic acid metabolic process organic acid metabolic process organic acid catabolic process formate catabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process small molecule metabolic process metabolic process cellular process response to stimulus response to stress response to wounding catabolic process oxoacid metabolic process carboxylic acid metabolic process organic acid metabolic process organic acid catabolic process formate catabolic 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	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle plastid cytosol chloroplast membraneless organelle intracellular membraneless organelle thylakoid

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR033689	NAD-dependent formate dehydrogenase	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR006139	D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR029752	D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR029753	D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.