› 6kdy

X-ray diffraction
3.02Å resolution

Crystal structure of the alpha bata heterodimer of human IDH3 in complex with NAD.

Released:
DOI: 10.2210/pdb6kdy/pdb
PDB entry 6kdy coloured by chain, front view.
PDB entry 6kdy coloured by chain, side view.
PDB entry 6kdy coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular basis for the function of the αβ heterodimer of human NAD-dependent isocitrate dehydrogenase.
Sun P, Ma T, Zhang T, Zhu H, Zhang J, Liu Y, Ding J
J Biol Chem 294 16214-16227 (2019)
PMID: 31515270

Function and Biology Details

Reaction catalysed: 
Isocitrate + NAD(+) = 2-oxoglutarate + CO(2) + NADH
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129150 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial Chains: A, C, E, G
Molecule details ›
Chains: A, C, E, G
Length: 341 amino acids
Theoretical weight: 36.83 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P50213 (Residues: 28-366; Coverage: 93%)
Gene name: IDH3A
Sequence domains: Isocitrate/isopropylmalate dehydrogenase
Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial Chains: B, D, F, H
Molecule details ›
Chains: B, D, F, H
Length: 356 amino acids
Theoretical weight: 39.7 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O43837 (Residues: 35-374; Coverage: 88%)
Gene name: IDH3B
Sequence domains: Isocitrate/isopropylmalate dehydrogenase

Ligands and Environments


Cofactor: Ligand NAD 4 x NAD
4 bound ligands:
Ligand PG4 2 x PG4
Ligand 2PE 1 x 2PE
Ligand PE7 1 x PE7
Ligand P6G 1 x P6G
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: P21
Unit cell:
a: 99.46Å b: 162.979Å c: 114.407Å
α: 90° β: 100.31° γ: 90°
R-values:
R R work R free
0.2 0.197 0.246
Expression system: Escherichia coli

Quick links

Citations

3 review citations

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

2 mentions without citation

Molecular basis for the function of the αβ heterodimer of human NAD-dependent isocitrate dehydrogenase.
Sun et al. (2019)
1 more