Crystal structure of choline oxidase reveals insights into the catalytic mechanism

Structure

x-ray diffraction · 2 distinct chains · 26% helix, 25% strand (DSSP).

Ligands and binding sites

• FAO · [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-[(4aS,10aR)-7,8-dimethyl-2,4-dioxo-1,3,4,4a,5,10a-hexahydrobenzo[g]pteridin-10(2H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate · ligand · 2 copies · chains A, B
• UNX · Unknown atom or ion · ion · 4 copies · chains A, B
• DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B

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

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1297 Ų buried · 16 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 2JBV · Crystal structure of choline oxidase reveals insights into the catalytic mechanism · the same entry in another collection · chain A against A, TM-score 1.00
• Q7X2H8 · AlphaFold monomer V2.0 prediction for choline oxidase (Q7X2H8) · 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 Q7X2H8
• Elsewhere: RCSB PDB 2JBV · PDBe 2JBV · UniProt Q7X2H8