› 2jkv

X-ray diffraction
2.53Å resolution

Structure of human Phosphogluconate Dehydrogenase in complex with NADPH at 2.53A

Released:
DOI: 10.2210/pdb2jkv/pdb
PDB entry 2jkv coloured by chain, front view.
PDB entry 2jkv coloured by chain, side view.
PDB entry 2jkv coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Pilka ES, Kavanagh KL, von Delft F, Muniz JRC, Murray J, Picaud S, Guo K, Edwards A, Arrowsmith CH, Weigelt J, Bountra C, Oppermann U

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
Molecule details ›
Chains: A, B, C, D, E, F
Length: 505 amino acids
Theoretical weight: 55.76 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P52209 (Residues: 1-483; Coverage: 100%)
Gene names: PGD, PGDH
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand NAP 5 x NAP
2 bound ligands:
Ligand CL 11 x CL
Ligand SO4 12 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P21
Unit cell:
a: 56.643Å b: 204.714Å c: 170.319Å
α: 90° β: 90.65° γ: 90°
R-values:
R R work R free
0.157 0.156 0.207
Expression system: Escherichia coli BL21(DE3)

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