X-ray crystal structure of 1-arachidonoyl glycerol bound to the cyclooxygenase channel of cyclooxygenase-2

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 9% strand (DSSP).

Ligands and binding sites

• AKR · Acrylic acid · ligand · 5 copies · chains A, B
• 1AG · (2S)-2,3-dihydroxypropyl (5Z,8Z,11Z,14Z)-icosa-5,8,11, 14-tetraenoate · ligand · 2 copies · chains A, B
• COH · Protoporphyrin IX containing co · ligand · 2 copies · chains A, B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
• MAN · alpha-D-mannopyranose · sugar
• GOL · Glycerol · additive · 3 copies · chains A, B
• BOG · octyl beta-D-glucopyranoside · additive · chains A

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 2660 Ų buried · 49 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 6 glycan (disulfide, N-glycosylation).

Compared structures

• 3MDL · X-ray crystal structure of 1-arachidonoyl glycerol bound to the cyclooxygenase channel of… · the same entry in another collection · chain A against A, TM-score 1.00
• Q05769 · AlphaFold monomer V2.0 prediction for prostaglandin G/H synthase 2 (Q05769) · 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 Q05769
• Elsewhere: RCSB PDB 3MDL · PDBe 3MDL · UniProt Q05769