› 5ofv

X-ray diffraction
1.5Å resolution

Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with 5-fluoro-2-methylbenzoic acid

Released:
DOI: 10.2210/pdb5ofv/pdb
PDB entry 5ofv coloured by chain, front view.
PDB entry 5ofv coloured by chain, side view.
PDB entry 5ofv coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Validating and enabling phosphoglycerate dehydrogenase (PHGDH) as a target for fragment-based drug discovery in PHGDH-amplified breast cancer.
Unterlass JE, Baslé A, Blackburn TJ, Tucker J, Cano C, Noble MEM, Curtin NJ
Oncotarget 9 13139-13153 (2018)
PMID: 29568346

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: 223 amino acids
Theoretical weight: 23.93 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O43175 (Residues: 93-315; Coverage: 42%)
Gene names: PGDH3, PHGDH
Sequence domains:
Structure domains: NAD(P)-binding Rossmann-like Domain

Ligands and Environments

1 bound ligand:
Ligand 9TZ 2 x 9TZ
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P1
Unit cell:
a: 43.342Å b: 45.608Å c: 56.269Å
α: 98.02° β: 111.14° γ: 105.85°
R-values:
R R work R free
0.226 0.224 0.273
Expression system: Escherichia coli

Quick links

Citations

6 review citations

Glucose Metabolism and Glucose Transporters in Breast Cancer.
Shin et al. (2021)
5 more