› 3h9e

X-ray diffraction
1.72Å resolution

Crystal structure of human sperm-specific glyceraldehyde-3-phosphate dehydrogenase (GAPDS) complex with NAD and phosphate

Released:
DOI: 10.2210/pdb3h9e/pdb
PDB entry 3h9e coloured by chain, front view.
PDB entry 3h9e coloured by chain, side view.
PDB entry 3h9e coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure and kinetic characterization of human sperm-specific glyceraldehyde-3-phosphate dehydrogenase, GAPDS.
Chaikuad A, Shafqat N, Al-Mokhtar R, Cameron G, Clarke AR, Brady RL, Oppermann U, Frayne J, Yue WW
Biochem J 435 401-9 (2011)
PMID: 21269272

Function and Biology Details

Reaction catalysed: 
D-glyceraldehyde 3-phosphate + phosphate + NAD(+) = 3-phospho-D-glyceroyl phosphate + NADH
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-127002 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glyceraldehyde-3-phosphate dehydrogenase, testis-specific Chains: O, P
Molecule details ›
Chains: O, P
Length: 346 amino acids
Theoretical weight: 37.84 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O14556 (Residues: 69-407; Coverage: 83%)
Gene names: GAPD2, GAPDH2, GAPDHS, GAPDS, HSD-35, HSD35
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand NAD 2 x NAD
2 bound ligands:
Ligand PO4 4 x PO4
Ligand EDO 14 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: C2
Unit cell:
a: 141.96Å b: 71.78Å c: 81.26Å
α: 90° β: 122.9° γ: 90°
R-values:
R R work R free
0.143 0.143 0.176
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Deregulation of glycolysis in cancer: glyceraldehyde-3-phosphate dehydrogenase as a therapeutic target.
Krasnov et al. (2013)
2 more

9 mentions without citation

Structure of insoluble rat sperm glyceraldehyde-3-phosphate dehydrogenase (GAPDH) via heterotetramer formation with Escherichia coli GAPDH reveals target for contraceptive design.
Frayne et al. (2009)
8 more