› 2g76

X-ray diffraction
1.7Å resolution

Crystal structure of human 3-phosphoglycerate dehydrogenase

Released:
DOI: 10.2210/pdb2g76/pdb
PDB entry 2g76 coloured by chain, front view.
PDB entry 2g76 coloured by chain, side view.
PDB entry 2g76 coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Turnbull AP, Salah E, Savitsky P, Gileadi O, von Delft F, Edwards A, Arrowsmith C, Weigelt J, Sundstrom M, Oppermann U, Structural Genomics Consortium (SGC)

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: 335 amino acids
Theoretical weight: 36.1 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O43175 (Residues: 4-315; Coverage: 59%)
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 MLT 2 x MLT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P21
Unit cell:
a: 43.084Å b: 124.113Å c: 59.502Å
α: 90° β: 100.99° γ: 90°
R-values:
R R work R free
0.183 0.181 0.216
Expression system: Escherichia coli

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