› 3mas

X-ray diffraction
3.2Å resolution

Crystal structure of heterodimeric R132H mutant of human cytosolic NADP(+)-dependent isocitrate dehydrogenase in complex with NADP and isocitrate

Released:
DOI: 10.2210/pdb3mas/pdb
PDB entry 3mas coloured by chain, front view.
PDB entry 3mas coloured by chain, side view.
PDB entry 3mas coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular mechanisms of "off-on switch" of activities of human IDH1 by tumor-associated mutation R132H.
Yang B, Zhong C, Peng Y, Lai Z, Ding J
Cell Res 20 1188-200 (2010)
PMID: 20975740

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:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-131148 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Isocitrate dehydrogenase [NADP] cytoplasmic Chain: A
Molecule details ›
Chain: A
Length: 422 amino acids
Theoretical weight: 47.77 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
Isocitrate dehydrogenase [NADP] cytoplasmic Chain: B
Molecule details ›
Chain: B
Length: 419 amino acids
Theoretical weight: 47.24 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 2 x NAP
1 bound ligand:
Ligand ICT 2 x ICT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P43212
Unit cell:
a: 83.136Å b: 83.136Å c: 308.508Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.235 0.233 0.283
Expression system: Escherichia coli

Quick links

Citations

20 review citations

IDH1 and IDH2 mutations in gliomas.
Cohen et al. (2013)
19 more

6 mentions without citation

IDH mutation in glioma: molecular mechanisms and potential therapeutic targets.
Han et al. (2020)
5 more