› 4aj3

X-ray diffraction
1.9Å resolution

3D structure of E. coli Isocitrate Dehydrogenase in complex with Isocitrate, calcium(II) and NADP - The pseudo-Michaelis complex

Released:
DOI: 10.2210/pdb4aj3/pdb
PDB entry 4aj3 coloured by chain, front view.
PDB entry 4aj3 coloured by chain, side view.
PDB entry 4aj3 coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Induced fit and the catalytic mechanism of isocitrate dehydrogenase.
Gonçalves S, Miller SP, Carrondo MA, Dean AM, Matias PM
Biochemistry 51 7098-115 (2012)
PMID: 22891681

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-140025 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Isocitrate dehydrogenase [NADP] Chain: A
Molecule details ›
Chain: A
Length: 416 amino acids
Theoretical weight: 45.81 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P08200 (Residues: 1-416; Coverage: 100%)
Gene names: JW1122, b1136, icd, icdA, icdE
Sequence domains: Isocitrate/isopropylmalate dehydrogenase
Structure domains: Isopropylmalate Dehydrogenase

Ligands and Environments


Cofactor: Ligand NAP 1 x NAP
2 bound ligands:
Ligand ICT 1 x ICT
Ligand CA 1 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BRUKER AXS MICROSTAR
Spacegroup: P43212
Unit cell:
a: 105.297Å b: 105.297Å c: 145.723Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.19 0.189 0.224
Expression system: Escherichia coli

Quick links

Citations

2 review citations

6-Phosphogluconate dehydrogenase and its crystal structures.
Hanau et al. (2022)
1 more

6 mentions without citation

Induced fit and the catalytic mechanism of isocitrate dehydrogenase.
Gonçalves et al. (2012)
5 more