› 5uq9

X-ray diffraction
3Å resolution

Crystal structure of 6-phosphogluconate dehydrogenase with ((4R,5R)-5-(hydroxycarbamoyl)-2,2-dimethyl-1,3-dioxolan-4-yl)methyl dihydrogen phosphate

Released:
DOI: 10.2210/pdb5uq9/pdb
PDB entry 5uq9 coloured by chain, front view.
PDB entry 5uq9 coloured by chain, side view.
PDB entry 5uq9 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Functional Genomics Reveals Synthetic Lethality between Phosphogluconate Dehydrogenase and Oxidative Phosphorylation.
Sun Y, Bandi M, Lofton T, Smith M, Bristow CA, Carugo A, Rogers N, Leonard P, Chang Q, Mullinax R, Han J, Shi X, Seth S, Meyers BA, Miller M, Miao L, Ma X, Feng N, Giuliani V, Geck Do M, Czako B, Palmer WS, Mseeh F, Asara JM, Jiang Y, Morlacchi P, Zhao S, Peoples M, Tieu TN, Warmoes MO, Lorenzi PL, Muller FL, DePinho RA, Draetta GF, Toniatti C, Jones P, Heffernan TP, Marszalek JR
Cell Rep 26 469-482.e5 (2019)
PMID: 30625329

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-156481 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
6-phosphogluconate dehydrogenase, decarboxylating Chains: A, B, C, D, E, F, G, H
Molecule details ›
Chains: A, B, C, D, E, F, G, H
Length: 489 amino acids
Theoretical weight: 53.76 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P52209 (Residues: 1-483; Coverage: 100%)
Gene names: PGD, PGDH
Sequence domains:
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand 8HS 1 x 8HS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.3.1
Spacegroup: P21
Unit cell:
a: 87.311Å b: 164.93Å c: 133.199Å
α: 90° β: 91.43° γ: 90°
R-values:
R R work R free
0.22 0.217 0.272
Expression system: Escherichia coli

Quick links

Citations

7 review citations

Targeting Metabolism in Cancer Cells and the Tumour Microenvironment for Cancer Therapy.
Li et al. (2020)
6 more

2 mentions without citation

Discovery of Ebselen as an Inhibitor of 6PGD for Suppressing Tumor Growth.
Feng et al. (2020)
1 more