› 4kzo

X-ray diffraction
2.2Å resolution

Crystal Structure Analysis of human IDH1 mutants in complex with NADP+ and Ca2+/alpha-Ketoglutarate

Released:
DOI: 10.2210/pdb4kzo/pdb
PDB entry 4kzo coloured by chain, front view.
PDB entry 4kzo coloured by chain, side view.
PDB entry 4kzo coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Mutant IDH1 enhances the production of 2-hydroxyglutarate due to its kinetic mechanism.
Rendina AR, Pietrak B, Smallwood A, Zhao H, Qi H, Quinn C, Adams ND, Concha N, Duraiswami C, Thrall SH, Sweitzer S, Schwartz B
Biochemistry 52 4563-77 (2013)
PMID: 23731180

Function and Biology Details

Reaction catalysed: 
(1a) isocitrate + NADP(+) = 2-oxalosuccinate + NADPH
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-131150 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Isocitrate dehydrogenase [NADP] cytoplasmic Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 425 amino acids
Theoretical weight: 48.14 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O75874 (Residues: 1-414; Coverage: 100%)
Gene names: IDH1, PICD
Sequence domains: Isocitrate/isopropylmalate dehydrogenase
Structure domains: Isopropylmalate Dehydrogenase

Ligands and Environments


Cofactor: Ligand NAP 3 x NAP
3 bound ligands:
Ligand CA 3 x CA
Ligand AKG 3 x AKG
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-D
Spacegroup: C2221
Unit cell:
a: 96.36Å b: 274.598Å c: 115.99Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.18 0.178 0.221
Expression system: Escherichia coli

Quick links

Citations

11 review citations

Metabolic consequences of oncogenic IDH mutations.
Parker et al. (2015)
10 more

9 mentions without citation

Isocitrate Dehydrogenase Mutations in Glioma: Genetics, Biochemistry, and Clinical Indications.
Liu et al. (2020)
8 more