The crystal structure of human ornithine aminotransferase with an intermediate bound during inactivation by (1S,3S)-3-amino-4- (hexafluoropropan-2-ylidenyl)-cyclopentane-1-carboxylic acid.

Structure

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

Ligands and binding sites

• IF1 · (1S,3S,4S)-3-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-4-(1,1,3,3,3-pentafluoroprop-1-en-2-yl)cyclopentane-1-carboxylic acid · ligand · 3 copies · chains A, B, C
• VLS · N-[1,3-dihydroxy-2-(hydroxymethyl)propan-2-yl]glycine · ligand · 2 copies · chains A, C

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

2 interfaces between chains.

• A–C · 676 Ų buried · 9 hydrogen bonds · protein-protein
• B–C · 495 Ų buried · 5 hydrogen bonds · protein-protein

Compared structures

• 7JX9 · The crystal structure of human ornithine aminotransferase with an intermediate bound… · 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 A 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 7JX9 · PDBe 7JX9 · UniProt P04181