› 5n6c

X-ray diffraction
2.3Å resolution

Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with NAD and L-Tartrate

Released:
DOI: 10.2210/pdb5n6c/pdb
PDB entry 5n6c coloured by chain, front view.
PDB entry 5n6c coloured by chain, side view.
PDB entry 5n6c coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural insights into the enzymatic activity and potential substrate promiscuity of human 3-phosphoglycerate dehydrogenase (PHGDH).
Unterlass JE, Wood RJ, Baslé A, Tucker J, Cano C, Noble MME, Curtin NJ
Oncotarget 8 104478-104491 (2017)
PMID: 29262655

Function and Biology Details

Reactions catalysed: 
(S)-malate + NAD(+) = oxaloacetate + NADH
(R)-2-hydroxyglutarate + NAD(+) = 2-oxoglutarate + NADH
3-phospho-D-glycerate + NAD(+) = 3-phosphonooxypyruvate + NADH
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128865 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-3-phosphoglycerate dehydrogenase Chains: A, B
Molecule details ›
Chains: A, B
Length: 300 amino acids
Theoretical weight: 32.16 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O43175 (Residues: 8-306; Coverage: 56%)
Gene names: PGDH3, PHGDH
Sequence domains:
Structure domains: NAD(P)-binding Rossmann-like Domain

Ligands and Environments


Cofactor: Ligand NAD 2 x NAD
1 bound ligand:
Ligand TLA 1 x TLA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P21
Unit cell:
a: 43.523Å b: 109.719Å c: 66.923Å
α: 90° β: 94.4° γ: 90°
R-values:
R R work R free
0.215 0.213 0.255
Expression system: Escherichia coli

Quick links

Citations

4 review citations

The Role of D-3-Phosphoglycerate Dehydrogenase in Cancer.
Zhao et al. (2020)
3 more

4 mentions without citation

CSN6 drives carcinogenesis by positively regulating Myc stability.
Chen et al. (2014)
3 more