› 1wpq

X-ray diffraction
2.5Å resolution

Ternary Complex Of Glycerol 3-phosphate Dehydrogenase 1 with NAD and dihydroxyactone

Released:
DOI: 10.2210/pdb1wpq/pdb
PDB entry 1wpq coloured by chain, front view.
PDB entry 1wpq coloured by chain, side view.
PDB entry 1wpq coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structures of human glycerol 3-phosphate dehydrogenase 1 (GPD1).
Ou X, Ji C, Han X, Zhao X, Li X, Mao Y, Wong LL, Bartlam M, Rao Z
J Mol Biol 357 858-69 (2006)
PMID: 16460752

Function and Biology Details

Reaction catalysed: 
sn-glycerol 3-phosphate + NAD(+) = glycerone phosphate + NADH
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-149368 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmic Chains: A, B
Molecule details ›
Chains: A, B
Length: 349 amino acids
Theoretical weight: 37.63 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P21695 (Residues: 1-349; Coverage: 100%)
Gene name: GPD1
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand NAD 2 x NAD
2 bound ligands:
Ligand SO4 7 x SO4
Ligand 13P 2 x 13P
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P43212
Unit cell:
a: 115.995Å b: 115.995Å c: 153.72Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.267 0.258 0.294
Expression system: Escherichia coli

Quick links

Citations

6 review citations

A role for flexible loops in enzyme catalysis.
Malabanan et al. (2010)
5 more

12 mentions without citation

A reevaluation of the origin of the rate acceleration for enzyme-catalyzed hydride transfer.
Reyes et al. (2017)
11 more