› 5n53

X-ray diffraction
1.48Å resolution

Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with N-(3-chloro-4-methoxyphenyl) acetamide

Released:
DOI: 10.2210/pdb5n53/pdb
PDB entry 5n53 coloured by chain, front view.
PDB entry 5n53 coloured by chain, side view.
PDB entry 5n53 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: 195 amino acids
Theoretical weight: 20.95 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O43175 (Residues: 100-294; Coverage: 37%)
Gene names: PGDH3, PHGDH
Sequence domains:
Structure domains: NAD(P)-binding Rossmann-like Domain

Ligands and Environments

1 bound ligand:
Ligand 8NB 2 x 8NB
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P1
Unit cell:
a: 43.353Å b: 45.323Å c: 55.255Å
α: 97.9° β: 110.06° γ: 106.35°
R-values:
R R work R free
0.192 0.189 0.244
Expression system: Escherichia coli

Quick links

Citations

6 review citations

The ins and outs of serine and glycine metabolism in cancer.
Geeraerts et al. (2021)
5 more