Annotations: 7CVP

The Crystal Structure of human PHGDH from Biortus.

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8080417	3000044	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8080417	3000044	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		e7cvpB1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F:	ECOD (v295.2)
A		e7cvpA1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F:	ECOD (v295.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02826	D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain (2-Hacid_dh_C)	D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain	This domain is inserted into the catalytic domain, the large dehydrogenase and D-lactate dehydrogenase families in SCOP. N-terminal portion of which is represented by family Pfam:PF00389.	Domain
A, B	PF00389	D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain (2-Hacid_dh)	D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain	This family represents the largest portion of the catalytic domain of 2-hydroxyacid dehydrogenases as the NAD binding domain is inserted within the structural domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	D-3-phosphoglycerate dehydrogenase	L-malate dehydrogenase (NAD+) 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 malate dehydrogenase activity catalytic activity (R)-2-hydroxyglutarate (NAD+) dehydrogenase activity (R)-2-hydroxyglutarate dehydrogenase activity phosphoglycerate dehydrogenase activity NAD binding binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding L-malate dehydrogenase (NAD+) 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 malate dehydrogenase activity catalytic activity (R)-2-hydroxyglutarate (NAD+) dehydrogenase activity (R)-2-hydroxyglutarate dehydrogenase activity phosphoglycerate dehydrogenase activity NAD binding binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding small molecule binding electron transfer activity	developmental process multicellular organismal process head development animal organ development brain development nervous system development multicellular organism development central nervous system development anatomical structure development animal gross anatomical part developmental process system development oxoacid metabolic process small molecule biosynthetic process carboxylic acid metabolic process developmental process multicellular organismal process head development animal organ development brain development nervous system development multicellular organism development central nervous system development anatomical structure development animal gross anatomical part developmental process system development oxoacid metabolic process small molecule biosynthetic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process L-serine metabolic process L-serine biosynthetic process carboxylic acid biosynthetic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process metabolic process cellular process small molecule metabolic process serine family amino acid biosynthetic process	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR029009	Allosteric substrate binding domain superfamily	Homologous Superfamily
A, B	IPR006139	D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain	Domain
A, B	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B	IPR029752	D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1	Conserved Site
A, B	IPR006236	D-3-phosphoglycerate dehydrogenase	Family
A, B	IPR029753	D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site	Conserved Site
A, B	IPR045626	D-3-phosphoglycerate dehydrogenase, ASB domain	Domain
A, B	IPR006140	D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	: O43175	PHGDH deficiency melanoma Neu-Laxova syndrome 1 non-small cell lung carcinoma Neu-Laxova syndrome prostate cancer liver cancer breast carcinoma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia 3-phosphoglycerate dehydrogenase deficiency Cell Transformation, Neoplastic retinal disease cutaneous melanoma PHGDH deficiency melanoma Neu-Laxova syndrome 1 non-small cell lung carcinoma Neu-Laxova syndrome prostate cancer liver cancer breast carcinoma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia 3-phosphoglycerate dehydrogenase deficiency Cell Transformation, Neoplastic retinal disease cutaneous melanoma intellectual disability malignant mesothelioma pancreatic ductal adenocarcinoma breast cancer subependymal giant cell astrocytoma interstitial cystitis liver neoplasm pancreatic intraductal papillary-mucinous carcinoma polycystic ovary syndrome psoriasis cutaneous lupus erythematosus inborn errors of metabolism leukodystrophy malignant ependymoma malignant pancreatic neoplasm

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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.