› 5grf

X-ray diffraction
2.5Å resolution

Crystal structure of the alpha gamma mutant (gamma-K151A) of human IDH3 in complex with Mg(2+), citrate and ADP

Released:
DOI: 10.2210/pdb5grf/pdb
PDB entry 5grf coloured by chain, front view.
PDB entry 5grf coloured by chain, side view.
PDB entry 5grf coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular mechanism of the allosteric regulation of the αγ heterodimer of human NAD-dependent isocitrate dehydrogenase.
Ma T, Peng Y, Huang W, Ding J
Sci Rep 7 40921 (2017)
PMID: 28098230

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-156145 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial Chain: A
Molecule details ›
Chain: A
Length: 339 amino acids
Theoretical weight: 36.68 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P50213 (Residues: 28-366; Coverage: 93%)
Gene name: IDH3A
Sequence domains: Isocitrate/isopropylmalate dehydrogenase
Structure domains: Isopropylmalate Dehydrogenase
Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial Chain: B
Molecule details ›
Chain: B
Length: 354 amino acids
Theoretical weight: 38.81 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P51553 (Residues: 40-393; Coverage: 90%)
Gene name: IDH3G
Sequence domains: Isocitrate/isopropylmalate dehydrogenase
Structure domains: Isopropylmalate Dehydrogenase

Ligands and Environments

3 bound ligands:
Ligand CIT 1 x CIT
Ligand ADP 1 x ADP
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P3121
Unit cell:
a: 114.336Å b: 114.336Å c: 143.901Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.209 0.207 0.248
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Redox regulation of the immune response.
Morris et al. (2022)
1 more

2 mentions without citation

Molecular mechanism of the allosteric regulation of the αγ heterodimer of human NAD-dependent isocitrate dehydrogenase.
Ma et al. (2017)
1 more