5LOA | pdb_00005loa

Crystal structure of the engineered D-Amino Acid Dehydrogenase (DAADH) bound to NADP+

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)
B	SCOP2B Superfamily	GAPDH-like	8058138	3000043	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	GAPDH-like	8058138	3000043	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)
B	Sel1	e5loaB1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sel1	ECOD (v294.1)
A	Sel1	e5loaA1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sel1	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	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)
A	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF16654	Diaminopimelic acid dehydrogenase C-terminal domain (DAPDH_C)	Diaminopimelic acid dehydrogenase C-terminal domain	This family comprises the C-terminal domain of diaminopimelic acid dehydrogenase. Diaminopimelate dehydrogenase is a NADPH-dependent enzyme that catalyzes the oxidative deamination of meso-2,6-diaminopimelate, which is the direct precursor of L-lysin ...	This family comprises the C-terminal domain of diaminopimelic acid dehydrogenase. Diaminopimelate dehydrogenase is a NADPH-dependent enzyme that catalyzes the oxidative deamination of meso-2,6-diaminopimelate, which is the direct precursor of L-lysine in bacterial lysine biosynthesis.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Meso-diaminopimelate D-dehydrogenase	oxidoreductase activity, acting on the CH-NH2 group of donors oxidoreductase activity diaminopimelate dehydrogenase activity oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor catalytic activity	diaminopimelate biosynthetic process oxoacid metabolic process small molecule biosynthetic process dicarboxylic acid metabolic process lipid biosynthetic process carboxylic acid metabolic process fatty acid derivative biosynthetic process primary metabolic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process carboxylic acid biosynthetic process fatty acid derivative metabolic process amino acid biosynthetic process biosynthetic process diaminopimelate biosynthetic process oxoacid metabolic process small molecule biosynthetic process dicarboxylic acid metabolic process lipid biosynthetic process carboxylic acid metabolic process fatty acid derivative biosynthetic process primary metabolic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process carboxylic acid biosynthetic process fatty acid derivative metabolic process amino acid biosynthetic process biosynthetic process metabolic process cellular process small molecule metabolic process dicarboxylic acid biosynthetic process lipid metabolic process lysine metabolic process L-lysine biosynthetic process aspartate family amino acid biosynthetic process alpha-amino acid metabolic process L-lysine biosynthetic process via diaminopimelate L-amino acid biosynthetic process L-amino acid metabolic process proteinogenic amino acid metabolic process proteinogenic amino acid biosynthetic process alpha-amino acid biosynthetic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B	IPR032094	Meso-diaminopimelate D-dehydrogenase, C-terminal	Domain
A, B	IPR010190	Diaminopimelate dehydrogenase, Ddh	Family

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.