3QY9 | pdb_00003qy9

The Crystal Structure of Dihydrodipicolinate reductase from Staphylococcus aureus

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
D	SCOP2B Superfamily	GAPDH-like	8089542	3000043	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	GAPDH-like	8089542	3000043	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	GAPDH-like	8089542	3000043	SCOP2B (2022-06-29)
A	SCOP2 Family	Dihydrodipicolinate reductase-like	8089541	4000095	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	GAPDH-like	8089542	3000043	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)
D	DapB_C	e3qy9D1	A: a+b two layers	X: FwdE/GAPDH domain-like	H: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain (From Topology)	T: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	F: DapB_C	ECOD (1.6)
D	DapB_N	e3qy9D2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: DapB_N	ECOD (1.6)
C	DapB_C	e3qy9C1	A: a+b two layers	X: FwdE/GAPDH domain-like	H: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain (From Topology)	T: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	F: DapB_C	ECOD (1.6)
C	DapB_N	e3qy9C2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: DapB_N	ECOD (1.6)
B	DapB_C	e3qy9B1	A: a+b two layers	X: FwdE/GAPDH domain-like	H: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain (From Topology)	T: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	F: DapB_C	ECOD (1.6)
B	DapB_N	e3qy9B2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: DapB_N	ECOD (1.6)
A	DapB_C	e3qy9A1	A: a+b two layers	X: FwdE/GAPDH domain-like	H: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain (From Topology)	T: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	F: DapB_C	ECOD (1.6)
A	DapB_N	e3qy9A2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: DapB_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.2.0)
D	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.2.0)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.2.0)
C	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.2.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.2.0)
B	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.2.0)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.2.0)
A	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.2.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Dihydrodipicolinate reductase	binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on the CH-CH group of donors catalytic activity 4-hydroxy-tetrahydrodipicolinate reductase oxidoreductase activity, acting on CH or CH2 groups binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on the CH-CH group of donors catalytic activity 4-hydroxy-tetrahydrodipicolinate reductase oxidoreductase activity, acting on CH or CH2 groups oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor NAD binding identical protein binding protein binding	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 aspartate family amino acid biosynthetic process alpha-amino acid metabolic process lysine biosynthetic process L-amino acid biosynthetic process L-amino acid metabolic process proteinogenic amino acid metabolic process lysine biosynthetic process via diaminopimelate proteinogenic amino acid biosynthetic process alpha-amino acid biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR000846	Dihydrodipicolinate reductase, N-terminal	Domain
A, B, C, D	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR022663	Dihydrodipicolinate reductase, C-terminal	Domain
A, B, C, D	IPR023940	Dihydrodipicolinate reductase	Family
A, B, C, D	IPR022664	Dihydrodipicolinate reductase, conserved site	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.