› 4yb4

X-ray diffraction
2.5Å resolution

Crystal structure of homoisocitrate dehydrogenase from Thermus thermophilus in complex with homoisocitrate, magnesium ion (II) and NADH

Released:
DOI: 10.2210/pdb4yb4/pdb
PDB entry 4yb4 coloured by chain, front view.
PDB entry 4yb4 coloured by chain, side view.
PDB entry 4yb4 coloured by chain, top view.
Source organism: Thermus thermophilus HB27
Entry authors: Takahashi K, Tomita T, Kuzuyama T, Nishiyama M

Function and Biology Details

Reaction catalysed: 
(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate + NAD(+) = 2-oxoadipate + CO(2) + NADH
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-180847 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Isocitrate/homoisocitrate dehydrogenase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 334 amino acids
Theoretical weight: 35.97 KDa
Source organism: Thermus thermophilus HB27
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q72IW9 (Residues: 1-334; Coverage: 100%)
Gene names: TT_C1012, hdh, hicd, hicdh
Sequence domains: Isocitrate/isopropylmalate dehydrogenase
Structure domains: Isopropylmalate Dehydrogenase

Ligands and Environments


Cofactor: Ligand NAI 4 x NAI
4 bound ligands:
Ligand MG 4 x MG
Ligand 48Y 4 x 48Y
Ligand GOL 24 x GOL
Ligand SO4 30 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P43212
Unit cell:
a: 159.663Å b: 159.663Å c: 148.517Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.153 0.15 0.205
Expression system: Escherichia coli BL21(DE3)

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