› 5yvt

X-ray diffraction
2.4Å resolution

Crystal structure of the alpha gamma heterodimer of human IDH3 in complex with Mg(2+) and NADH

Released:
DOI: 10.2210/pdb5yvt/pdb
PDB entry 5yvt coloured by chain, front view.
PDB entry 5yvt coloured by chain, side view.
PDB entry 5yvt coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Insights into the inhibitory mechanisms of NADH on the αγ heterodimer of human NAD-dependent isocitrate dehydrogenase.
Liu Y, Hu L, Ma T, Yang J, Ding J
Sci Rep 8 3146 (2018)
PMID: 29453450

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: 38.87 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


Cofactor: Ligand NAI 2 x NAI
1 bound ligand:
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: 118.027Å b: 118.027Å c: 142.109Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.213 0.211 0.236
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

Regulation and function of the mammalian tricarboxylic acid cycle.
Arnold et al. (2023)
2 more

2 mentions without citation

Insights into the inhibitory mechanisms of NADH on the αγ heterodimer of human NAD-dependent isocitrate dehydrogenase.
Liu et al. (2018)
1 more