4YDR | pdb_00004ydr

Crystal structure of oxidized homoserine dehydrogenase of Sulfolobus tokodaii

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	Homoserine dehydrogenase-like	8097787	4000093	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	GAPDH-like	8097788	3000043	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	GAPDH-like	8097788	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)
A		e4ydrA1	A: OB-fold	X: Rubredoxin-related	H: Rubredoxin-related	T: Protoglobin	F:	ECOD (20:10:01)
B		e4ydrB1	A: OB-fold	X: Rubredoxin-related	H: Rubredoxin-related	T: Protoglobin	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF03447	Homoserine dehydrogenase, NAD binding domain (NAD_binding_3)	Homoserine dehydrogenase, NAD binding domain	This domain adopts a Rossmann NAD binding fold. The C-terminal domain of homoserine dehydrogenase contributes a single helix to this structural domain, which is not included in the Pfam model.	Domain
A, B	PF00742	Homoserine dehydrogenase (Homoserine_dh)	Homoserine dehydrogenase		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Homoserine dehydrogenase	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-OH group of donors, NAD or NADP as acceptor homoserine dehydrogenase activity oxidoreductase activity, acting on CH-OH group of donors catalytic activity cation binding 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-OH group of donors, NAD or NADP as acceptor homoserine dehydrogenase activity oxidoreductase activity, acting on CH-OH group of donors catalytic activity cation binding ion binding metal ion binding	oxoacid metabolic process small molecule biosynthetic process aspartate family amino acid biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process amino acid metabolic process primary metabolic process L-threonine metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process L-amino acid metabolic process carboxylic acid biosynthetic process proteinogenic amino acid metabolic process amino acid biosynthetic process oxoacid metabolic process small molecule biosynthetic process aspartate family amino acid biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process amino acid metabolic process primary metabolic process L-threonine metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process L-amino acid metabolic process carboxylic acid biosynthetic process proteinogenic amino acid metabolic process amino acid biosynthetic process L-threonine biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process metabolic process cellular process small molecule metabolic process alpha-amino acid biosynthetic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR019811	Homoserine dehydrogenase, conserved site	Conserved Site
A, B	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B	IPR001342	Homoserine dehydrogenase, catalytic	Domain
A, B	IPR022697	Homoserine dehydrogenase lacking ACT domain	Family
A, B	IPR005106	Aspartate/homoserine dehydrogenase, NAD-binding	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.