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

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 20% strand (DSSP).

Ligands and binding sites

• Y7S · (1~{R},3~{S},4~{R})-3-methyl-4-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]cyclopentane-1-carboxylic acid · ligand · 6 copies · chains B, C, E, F, I, J

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

Pockets

13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Interfaces

8 interfaces between chains.

• I–J · 5283 Ų buried · 81 hydrogen bonds · protein-protein
• E–F · 5272 Ų buried · 78 hydrogen bonds · protein-protein
• B–C · 5248 Ų buried · 77 hydrogen bonds · protein-protein
• B–J · 665 Ų buried · 6 hydrogen bonds · protein-protein
• C–E · 230 Ų buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 12 covalent (covalent ligand).

Compared structures

• 7LNM · Ornithine Aminotransferase (OAT) cocrystallized with its inactivator… · the same entry in another collection · chain E against E, 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 7LNM · PDBe 7LNM · UniProt P04181