› 4l06

X-ray diffraction
2.28Å resolution

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

Released:
DOI: 10.2210/pdb4l06/pdb
PDB entry 4l06 coloured by chain, front view.
PDB entry 4l06 coloured by chain, side view.
PDB entry 4l06 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, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 425 amino acids
Theoretical weight: 48.11 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 6 x NAP
2 bound ligands:
Ligand CA 6 x CA
Ligand AKG 6 x AKG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-D
Spacegroup: P212121
Unit cell:
a: 96.22Å b: 116.55Å c: 275.71Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.226 0.224 0.27
Expression system: Escherichia coli

Quick links

Citations

12 review citations

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

2 mentions without citation

Human Glycerol 3-Phosphate Dehydrogenase: X-ray Crystal Structures That Guide the Interpretation of Mutagenesis Studies.
Mydy et al. (2019)
1 more