3Q3C

Crystal structure of a serine dehydrogenase from Pseudomonas aeruginosa pao1 in complex with NAD

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3q3ca2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	Hydroxyisobutyrate and 6-phosphogluconate dehydrogenase domain	Hydroxyisobutyrate dehydrogenase	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
A	d3q3ca1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	6-phosphogluconate dehydrogenase-like, N-terminal domain	Hydroxyisobutyrate dehydrogenase	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	6-phosphogluconate dehydrogenase-like	8089691	3000048	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	NAD_binding_11	e3q3cA1	A: alpha arrays	X: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	H: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: NAD_binding_11	ECOD (1.6)
A	NAD_binding_2	e3q3cA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: NAD_binding_2	ECOD (1.6)

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	1.10.1040.10	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF03446	NAD binding domain of 6-phosphogluconate dehydrogenase (NAD_binding_2)	NAD binding domain of 6-phosphogluconate dehydrogenase	The NAD binding domain of 6-phosphogluconate dehydrogenase adopts a Rossmann fold.	Domain
A	PF14833	NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase (NAD_binding_11)	NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase	3-Hydroxyisobutyrate is a central metabolite in the valine catabolic pathway, and is reversibly oxidised to methylmalonate semi-aldehyde by a specific dehydrogenase belonging to the 3-hydroxyacid dehydrogenase family. The reaction is NADP-dependent a ...	3-Hydroxyisobutyrate is a central metabolite in the valine catabolic pathway, and is reversibly oxidised to methylmalonate semi-aldehyde by a specific dehydrogenase belonging to the 3-hydroxyacid dehydrogenase family. The reaction is NADP-dependent and this region of the enzyme binds NAD. The NAD-binding domain of 6-phosphogluconate dehydrogenase adopts an alpha helical structure [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Probable 3-hydroxyisobutyrate 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 binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding 3-hydroxyisobutyrate dehydrogenase activity 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 binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding 3-hydroxyisobutyrate dehydrogenase activity NAD binding	catabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process branched-chain amino acid catabolic process cellular catabolic process carboxylic acid catabolic process small molecule metabolic process metabolic process cellular process branched-chain amino acid metabolic process catabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process branched-chain amino acid catabolic process cellular catabolic process carboxylic acid catabolic process small molecule metabolic process metabolic process cellular process branched-chain amino acid metabolic process small molecule catabolic process amino acid catabolic process protein-containing complex organization protein homotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis serine family amino acid metabolic process L-serine catabolic process alpha-amino acid metabolic process L-amino acid catabolic process L-serine metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process serine family amino acid catabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR006115	6-phosphogluconate dehydrogenase, NADP-binding	Domain
A	IPR029154	3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain	Domain
A	IPR008927	6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily	Homologous Superfamily
A	IPR011548	3-hydroxyisobutyrate dehydrogenase	Family
A	IPR015815	3-hydroxyisobutyrate dehydrogenase-related	Family
A	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A	IPR013328	6-phosphogluconate dehydrogenase, domain 2	Homologous Superfamily
A	IPR002204	3-hydroxyisobutyrate dehydrogenase-related, 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.