4K28 | pdb_00004k28

2.15 Angstrom resolution crystal structure of a shikimate dehydrogenase family protein from Pseudomonas putida KT2440 in complex with NAD+

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)
A	SCOP2 Family	Shikimate 5-dehydrogenase (AroE)-like	8074743	4000101	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	MtdA-like	8074744	3000046	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	MtdA-like	8074744	3000046	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	Death	e4k28A1	A: a/b three-layered sandwiches	X: Tautomerase/MIF-like	H: Tautomerase/MIF	T: Catalytic domain of hepatitis C virus NS2-3 protease	F: Death	ECOD (v294.1)
B	SmpA_OmlA	e4k28B1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: SmpA_OmlA	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	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)
B	3.40.50.10860	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Leucine Dehydrogenase, chain A, domain 1	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF08501	Shikimate dehydrogenase substrate binding domain (Shikimate_dh_N)	Shikimate dehydrogenase substrate binding domain	This domain is the substrate binding domain of shikimate dehydrogenase [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Shikimate dehydrogenase family protein	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 shikimate 3-dehydrogenase (NADP+) activity catalytic activity binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding cation binding 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 shikimate 3-dehydrogenase (NADP+) activity catalytic activity binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding cation binding ion binding metal ion binding	oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process metabolic process cellular process shikimate metabolic process monocarboxylic acid metabolic process organic acid metabolic process small molecule biosynthetic process dicarboxylic acid metabolic process organic acid biosynthetic process carboxylic acid biosynthetic process chorismate metabolic process biosynthetic process oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process metabolic process cellular process shikimate metabolic process monocarboxylic acid metabolic process organic acid metabolic process small molecule biosynthetic process dicarboxylic acid metabolic process organic acid biosynthetic process carboxylic acid biosynthetic process chorismate metabolic process biosynthetic process chorismate biosynthetic process dicarboxylic acid biosynthetic process aromatic amino acid family biosynthetic process aromatic amino acid metabolic process amino acid metabolic process primary metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B	IPR046346	Aminoacid dehydrogenase-like, N-terminal domain superfamily	Homologous Superfamily
A, B	IPR022893	Shikimate dehydrogenase family	Family
A, B	IPR013708	Shikimate dehydrogenase substrate binding, N-terminal	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.