Crystal structure of N2C/D282C stabilized opsin bound to RS16

Structure

x-ray diffraction · 1 distinct chain · 69% helix, 4% strand (DSSP).

Ligands and binding sites

• ACE · Acetyl group · ligand · chains A
• PLM · Palmitic acid · ligand · chains A
• DL2 · 5-chloranyl-2-(2-oxidanylidene-2-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-yl-ethyl)-3~{H}-pyridin-6-one · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
• MAN · alpha-D-mannopyranose · sugar · 2 copies
• BMA · beta-D-mannopyranose · sugar
• BOG · octyl beta-D-glucopyranoside · additive · 5 copies · chains A

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Modifications

Observed in the structure: 2 covalent, 2 disulfide, 1 glycan, 1 lipid (disulfide, additive adduct, covalent ligand, N-glycosylation, palmitoylation).

Compared structures

• 6FKD · Crystal structure of N2C/D282C stabilized opsin bound to RS16 · the same entry in another collection · 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 P02699
• Elsewhere: RCSB PDB 6FKD · PDBe 6FKD · UniProt P02699