› 3vml

X-ray diffraction
1.56Å resolution

Chimera 3-isopropylmalate dehydrogenase between Shewanella oneidensis MR-1 (O) and Shewanella benthica DB21 MT-2 (M) from N-terminal: 20% O middle 70% M residual 10% O

Released:
DOI: 10.2210/pdb3vml/pdb
PDB entry 3vml coloured by chain, front view.
PDB entry 3vml coloured by chain, side view.
PDB entry 3vml coloured by chain, top view.
Source organisms:
Entry authors: Nagae T, Watanabe N

Function and Biology Details

Reaction catalysed: 
(1a) (2R,3S)-3-isopropylmalate + NAD(+) = (2S)-2-isopropyl-3-oxosuccinate + NADH
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-112454 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3-isopropylmalate dehydrogenase Chain: A
Molecule details ›
Chain: A
Length: 375 amino acids
Theoretical weight: 40.73 KDa
Source organisms: Expression system: Escherichia coli
UniProt:
  • Canonical: D2YZL2 (Residues: 2-25, 69-328; Coverage: 78%)
  • Canonical: Q8E9N3 (Residues: 26-68, 329-364; Coverage: 22%)
Gene names: SHEWBE_0188, SO_4235, leuB
Sequence domains: Isocitrate/isopropylmalate dehydrogenase
Structure domains: Isopropylmalate Dehydrogenase

Ligands and Environments

3 bound ligands:
Ligand IPM 1 x IPM
Ligand MG 1 x MG
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: C2221
Unit cell:
a: 89.008Å b: 107.523Å c: 83.109Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.179 0.177 0.209
Expression system: Escherichia coli

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