Crystal structure of unoccupied cyclooxygenase-1

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 8% strand (DSSP).

Ligands and binding sites

• HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
• NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 4 copies · chains A, B
• BMA · beta-D-mannopyranose · sugar · 3 copies · chains A
• MAN · alpha-D-mannopyranose · sugar · 2 copies · chains B
• BOG · octyl beta-D-glucopyranoside · additive · 5 copies · chains A, B
• GOL · Glycerol · additive · chains 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 · 2716 Ų buried · 31 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide, 6 glycan (disulfide, N-glycosylation).

Compared structures

• 3N8V · Crystal Structure of Unoccupied Cyclooxygenase-1 · the same entry in another collection · chain A against A, TM-score 1.00
• P05979 · AlphaFold monomer V2.0 prediction for prostaglandin G/H synthase 1 (P05979) · 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 P05979
• Elsewhere: RCSB PDB 3N8V · PDBe 3N8V · UniProt P05979