› 2r4j

X-ray diffraction
1.96Å resolution

Crystal structure of Escherichia coli SeMet substituted Glycerol-3-phosphate Dehydrogenase in complex with DHAP

Released:
DOI: 10.2210/pdb2r4j/pdb
PDB entry 2r4j coloured by chain, front view.
PDB entry 2r4j coloured by chain, side view.
PDB entry 2r4j coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Structure of glycerol-3-phosphate dehydrogenase, an essential monotopic membrane enzyme involved in respiration and metabolism.
Yeh JI, Chinte U, Du S
Proc Natl Acad Sci U S A 105 3280-5 (2008)
PMID: 18296637

Function and Biology Details

Reaction catalysed: 
sn-glycerol 3-phosphate + a quinone = glycerone phosphate + a quinol
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-146441 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Aerobic glycerol-3-phosphate dehydrogenase Chains: A, B
Molecule details ›
Chains: A, B
Length: 501 amino acids
Theoretical weight: 57.16 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P13035 (Residues: 1-501; Coverage: 100%)
Gene names: JW3389, b3426, glpD, glyD
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand FAD 2 x FAD
7 bound ligands:
Ligand BOG 6 x BOG
Ligand PO4 2 x PO4
Ligand EDO 26 x EDO
Ligand IMD 6 x IMD
Ligand 13P 2 x 13P
Ligand BCN 3 x BCN
Ligand TAM 1 x TAM
1 modified residue:
Ligand MSE 14 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: I222
Unit cell:
a: 113.916Å b: 114.142Å c: 193.591Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.214 0.211 0.263
Expression system: Escherichia coli

Quick links

Citations

11 review citations

The sites and topology of mitochondrial superoxide production.
Brand MD. (2010)
10 more

3 mentions without citation

Structure of glycerol-3-phosphate dehydrogenase, an essential monotopic membrane enzyme involved in respiration and metabolism.
Yeh et al. (2008)
2 more