› 8v9m

X-ray diffraction
1.61Å resolution

Human Ornithine Aminotransferase cocrystallized with its inhibitor, (R)-3-amino-5,5-difluorocyclohex-1-ene-1-carboxylic acid.

Released:
DOI: 10.2210/pdb8v9m/pdb
PDB entry 8v9m coloured by chain, front view.
PDB entry 8v9m coloured by chain, side view.
PDB entry 8v9m coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Design, Synthesis, and Mechanistic Studies of (R)-3-Amino-5,5-difluorocyclohex-1-ene-1-carboxylic Acid as an Inactivator of Human Ornithine Aminotransferase.
Devitt AN, Vargas AL, Zhu W, Des Soye BJ, Butun FA, Alt T, Kaley N, Ferreira GM, Moran GR, Kelleher NL, Liu D, Silverman RB
ACS Chem Biol (2024)
PMID: 38630468

Function and Biology Details

Reaction catalysed: 
L-ornithine + a 2-oxo acid = L-glutamate 5-semialdehyde + an L-amino acid
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-137491 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ornithine aminotransferase, mitochondrial Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 404 amino acids
Theoretical weight: 44.86 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P04181 (Residues: 36-439; Coverage: 92%)
Gene name: OAT
Sequence domains: Aminotransferase class-III

Ligands and Environments

2 bound ligands:
Ligand YR5 3 x YR5
Ligand GOL 4 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-D
Spacegroup: P3221
Unit cell:
a: 115.334Å b: 115.334Å c: 186.292Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.166 0.164 0.193
Expression system: Escherichia coli

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