X-ray diffraction
1.5Å resolution

Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with 3-Chloro-4-fluorobenzamide


Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Entry contents:
1 distinct polypeptide molecule
D-3-phosphoglycerate dehydrogenase Chains: A, B
Molecule details ›
Chains: A, B
Length: 223 amino acids
Theoretical weight: 23.93 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
  • Canonical: O43175 (Residues: 93-315; Coverage: 42%)
Gene names: PGDH3, PHGDH
Sequence domains: D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
Structure domains: NAD(P)-binding Rossmann-like Domain

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P1
Unit cell:
a: 43.386Å b: 45.835Å c: 55.996Å
α: 97.58° β: 111.01° γ: 106.01°
R R work R free
0.178 0.175 0.242
Expression system: Escherichia coli