› 7ce3

X-ray diffraction
3.47Å resolution

Crystal structure of human IDH3 holoenzyme in APO form.

Released:
DOI: 10.2210/pdb7ce3/pdb
PDB entry 7ce3 coloured by chain, front view.
PDB entry 7ce3 coloured by chain, side view.
PDB entry 7ce3 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure and allosteric regulation of human NAD-dependent isocitrate dehydrogenase.
Sun P, Liu Y, Ma T, Ding J
Cell Discov 6 94 (2020)
PMID: 33349631

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 tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129151 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial Chains: A, C
Molecule details ›
Chains: A, C
Length: 366 amino acids
Theoretical weight: 39.64 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P50213 (Residues: 1-366; Coverage: 100%)
Gene name: IDH3A
Sequence domains: Isocitrate/isopropylmalate dehydrogenase
Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial Chain: B
Molecule details ›
Chain: B
Length: 357 amino acids
Theoretical weight: 39.14 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P51553 (Residues: 40-393; Coverage: 90%)
Gene name: IDH3G
Sequence domains: Isocitrate/isopropylmalate dehydrogenase
Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial Chain: D
Molecule details ›
Chain: D
Length: 359 amino acids
Theoretical weight: 39.98 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

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: I4122
Unit cell:
a: 204.568Å b: 204.568Å c: 237.877Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.215 0.213 0.246
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Disrupted Alpha-Ketoglutarate Homeostasis: Understanding Kidney Diseases from the View of Metabolism and Beyond.
Guo et al. (2022)
4 other articles

4 mentions without citation

An evolving view of complex II-noncanonical complexes, megacomplexes, respiration, signaling, and beyond.
Iverson et al. (2023)
3 more