› 5yfm

X-ray diffraction
2.4Å resolution

Human isocitrate dehydrogenase 1 bound with NADP

Released:
DOI: 10.2210/pdb5yfm/pdb
PDB entry 5yfm coloured by chain, front view.
PDB entry 5yfm coloured by chain, side view.
PDB entry 5yfm coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Nordlund P, Chen D, Jansson A, Larsson A

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-131150 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Isocitrate dehydrogenase [NADP] cytoplasmic Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 414 amino acids
Theoretical weight: 46.72 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O75874 (Residues: 1-414; Coverage: 100%)
Gene names: IDH1, PICD
Sequence domains: Isocitrate/isopropylmalate dehydrogenase
Structure domains: Isopropylmalate Dehydrogenase

Ligands and Environments


Cofactor: Ligand NAP 3 x NAP
1 bound ligand:
Ligand MG 3 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: C2
Unit cell:
a: 203.02Å b: 85.58Å c: 86.07Å
α: 90° β: 98.08° γ: 90°
R-values:
R R work R free
0.177 0.173 0.239
Expression system: Escherichia coli

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