› 4gwk

X-ray diffraction
1.53Å resolution

Crystal structure of 6-phosphogluconate dehydrogenase complexed with 3-phosphoglyceric acid

Released:
DOI: 10.2210/pdb4gwk/pdb
PDB entry 4gwk coloured by chain, front view.
PDB entry 4gwk coloured by chain, side view.
PDB entry 4gwk coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Phosphoglycerate mutase 1 coordinates glycolysis and biosynthesis to promote tumor growth.
Hitosugi T, Zhou L, Elf S, Fan J, Kang HB, Seo JH, Shan C, Dai Q, Zhang L, Xie J, Gu TL, Jin P, Alečković M, LeRoy G, Kang Y, Sudderth JA, DeBerardinis RJ, Luan CH, Chen GZ, Muller S, Shin DM, Owonikoko TK, Lonial S, Arellano ML, Khoury HJ, Khuri FR, Lee BH, Ye K, Boggon TJ, Kang S, He C, Chen J
Cancer Cell 22 585-600 (2012)
PMID: 23153533

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

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-156480 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
6-phosphogluconate dehydrogenase, decarboxylating Chain: A
Molecule details ›
Chain: A
Length: 484 amino acids
Theoretical weight: 53.27 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P52209 (Residues: 2-483; Coverage: 100%)
Gene names: PGD, PGDH
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand 3PG 2 x 3PG
Ligand MES 2 x MES
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P43212
Unit cell:
a: 87.246Å b: 87.246Å c: 130.424Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.171 0.17 0.174
Expression system: Escherichia coli

Quick links

Citations

75 review citations

Serine, glycine and one-carbon units: cancer metabolism in full circle.
Locasale JW. (2013)
74 more

5 mentions without citation

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