› 1yba

X-ray diffraction
2.24Å resolution

The active form of phosphoglycerate dehydrogenase

Released:
DOI: 10.2210/pdb1yba/pdb
PDB 1yba coloured by chain and viewed from the front.
PDB 1yba coloured by chain and viewed from the side.
PDB 1yba coloured by chain and viewed from the top.
Source organism: Escherichia coli
Primary publication:
Vmax regulation through domain and subunit changes. The active form of phosphoglycerate dehydrogenase.
Thompson JR, Bell JK, Bratt J, Grant GA, Banaszak LJ
Biochemistry 44 5763-73 (2005)
PMID: 15823035

Function and Biology Details

Reactions catalysed: 
(R)-2-hydroxyglutarate + NAD(+) = 2-oxoglutarate + NADH
3-phospho-D-glycerate + NAD(+) = 3-phosphonooxypyruvate + NADH
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-3-phosphoglycerate dehydrogenase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 410 amino acids
Theoretical weight: 44.6 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P0A9T0 (Residues: 1-410; Coverage: 100%)
Gene names: JW2880, b2913, serA
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand NAD 4 x NAD
3 bound ligands:
Ligand PO4 5 x PO4
Ligand AKG 4 x AKG
Ligand UNL 7 x UNL
1 modified residue:
Ligand MSE 32 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P43
Unit cell:
a: 76.159Å b: 76.159Å c: 354.144Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.189 0.186 0.235
Expression system: Escherichia coli K-12

Quick links

Citations

5 review citations

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

14 mentions without citation

D-3-Phosphoglycerate Dehydrogenase.
Grant GA. (2018)
13 more