› 2zyd

X-ray diffraction
1.5Å resolution

Dimeric 6-phosphogluconate dehydrogenase complexed with glucose

Released:
DOI: 10.2210/pdb2zyd/pdb
PDB entry 2zyd coloured by chain, front view.
PDB entry 2zyd coloured by chain, side view.
PDB entry 2zyd coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Conformational changes associated with cofactor/substrate binding of 6-phosphogluconate dehydrogenase from Escherichia coli and Klebsiella pneumoniae: Implications for enzyme mechanism.
Chen YY, Ko TP, Chen WH, Lo LP, Lin CH, Wang AH
J Struct Biol 169 25-35 (2010)
PMID: 19686854

Function and Biology Details

Reaction catalysed: 
6-phospho-D-gluconate + NADP(+) = D-ribulose 5-phosphate + CO(2) + NADPH
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132424 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
6-phosphogluconate dehydrogenase, decarboxylating Chains: A, B
Molecule details ›
Chains: A, B
Length: 480 amino acids
Theoretical weight: 53.04 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P00350 (Residues: 1-468; Coverage: 100%)
Gene names: JW2011, b2029, gnd
Sequence domains:
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand GLO 1 x GLO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P212121
Unit cell:
a: 68.452Å b: 118.609Å c: 119.996Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.166 0.165 0.191
Expression system: Escherichia coli BL21(DE3)

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Citations

20 citation in other articles

Phosphoglycerate mutase 1 coordinates glycolysis and biosynthesis to promote tumor growth.
Hitosugi et al. (2012)
19 more

4 mentions without citation

6-Phosphogluconate dehydrogenase and its crystal structures.
Hanau et al. (2022)
3 more