Ornithine aminotransferase (oat) soaked with its inactivator - (1S, 3S)-3-amino-4-(DIFLUOROMETHYLENE)CYCLOHEXENE-1-carboxylic acid

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 18% strand (DSSP).

Ligands and binding sites

• THR · Threonine · ligand · 3 copies · chains A, B, C
• Y8P · (3~{S},4~{S})-4-methyl-3-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]cyclohexene-1-carboxylic acid · ligand · 2 copies · chains A, B
• YCD · (4~{R})-4-(fluoranylmethyl)-3-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]cyclohexene-1-carboxylic acid · ligand · chains C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Interfaces

2 interfaces between chains.

• A–C · 635 Ų buried · 6 hydrogen bonds · protein-protein
• B–C · 500 Ų buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

• 7LOM · Ornithine Aminotransferase (OAT) soaked with its inactivator… · the same entry in another collection · chain A against A, TM-score 1.00
• P04181 · AlphaFold monomer V2.0 prediction for ornithine aminotransferase, mitochondrial (P04181) · a predicted model of the same protein · chain B against A, TM-score 1.00

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P04181
• Elsewhere: RCSB PDB 7LOM · PDBe 7LOM · UniProt P04181