› 1t0l

X-ray diffraction
2.41Å resolution

Crystal structure of human cytosolic NADP(+)-dependent isocitrate dehydrogenase in complex with NADP, isocitrate, and calcium(2+)

Released:
DOI: 10.2210/pdb1t0l/pdb
PDB entry 1t0l coloured by chain, front view.
PDB entry 1t0l coloured by chain, side view.
PDB entry 1t0l coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structures of human cytosolic NADP-dependent isocitrate dehydrogenase reveal a novel self-regulatory mechanism of activity.
Xu X, Zhao J, Xu Z, Peng B, Huang Q, Arnold E, Ding J
J Biol Chem 279 33946-57 (2004)
PMID: 15173171

Function and Biology Details

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

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, D
Molecule details ›
Chains: A, B, C, D
Length: 414 amino acids
Theoretical weight: 46.72 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
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 4 x NAP
2 bound ligands:
Ligand CA 4 x CA
Ligand ICT 4 x ICT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU ULTRAX 18
Spacegroup: P21
Unit cell:
a: 103.298Å b: 86.738Å c: 115.766Å
α: 90° β: 107.15° γ: 90°
R-values:
R R work R free
0.214 0.214 0.253
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

72 review citations

What a difference a hydroxyl makes: mutant IDH, (R)-2-hydroxyglutarate, and cancer.
Losman et al. (2013)
71 more

31 mentions without citation

Isocitrate dehydrogenase 1 and 2 mutations in cancer: alterations at a crossroads of cellular metabolism.
Reitman et al. (2010)
30 more