› 4njm

X-ray diffraction
1.79Å resolution

Crystal Structure of phosphoglycerate bound 3-phosphoglycerate dehydrogenase in Entamoeba histolytica

Released:
DOI: 10.2210/pdb4njm/pdb
PDB entry 4njm coloured by chain, front view.
PDB entry 4njm coloured by chain, side view.
PDB entry 4njm coloured by chain, top view.
Source organism: Entamoeba histolytica
Primary publication:
Crystal structures and kinetics of Type III 3-phosphoglycerate dehydrogenase reveal catalysis by lysine.
Singh RK, Raj I, Pujari R, Gourinath S
FEBS J 281 5498-512 (2014)
PMID: 25294608

Function and Biology Details

Reaction catalysed: 
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:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-181165 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
D 3 phosphoglycerate dehydrogenase putative Chain: A
Molecule details ›
Chain: A
Length: 309 amino acids
Theoretical weight: 34.75 KDa
Source organism: Entamoeba histolytica
Expression system: Escherichia coli
UniProt:
  • Canonical: Q76KF5 (Residues: 1-299; Coverage: 100%)
Gene names: CL6EHI_060860, EhPGDH
Sequence domains:
Structure domains: NAD(P)-binding Rossmann-like Domain
D 3 phosphoglycerate dehydrogenase putative Chain: B
Molecule details ›
Chain: B
Length: 309 amino acids
Theoretical weight: 34.83 KDa
Source organism: Entamoeba histolytica
Expression system: Escherichia coli
UniProt:
  • Canonical: Q76KF5 (Residues: 1-299; Coverage: 100%)
Gene names: CL6EHI_060860, EhPGDH
Sequence domains:
Structure domains: NAD(P)-binding Rossmann-like Domain

Ligands and Environments

1 bound ligand:
Ligand 3PG 2 x 3PG
1 modified residue:
Ligand CME 1 x CME

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM14
Spacegroup: P21
Unit cell:
a: 50.718Å b: 77.346Å c: 89.925Å
α: 90° β: 101.78° γ: 90°
R-values:
R R work R free
0.206 0.204 0.241
Expression system: Escherichia coli

Quick links

Citations

1 review citation

D-3-Phosphoglycerate Dehydrogenase.
Grant GA. (2018)
6 other articles