Crystal structure of the active G-protein-coupled receptor opsin in complex with the finger-loop peptide derived from the full-length arrestin-1

Structure

x-ray diffraction · 2 distinct chains · 71% helix, 4% strand (DSSP).

Ligands and binding sites

• PLM · Palmitic acid · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
• GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
• BMA · beta-D-mannopyranose · sugar
• MAN · alpha-D-mannopyranose · sugar
• SO4 · Sulfate ion · ion · chains A
• BOG · octyl beta-D-glucopyranoside · additive · 3 copies · chains A
• ACT · Acetate ion · additive · chains A

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 447 Ų buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide, 1 glycan, 1 lipid (disulfide, N-glycosylation, palmitoylation).

Compared structures

• 4PXF · Crystal structure of the active G-protein-coupled receptor opsin in complex with the… · the same entry in another collection · chain A against A, TM-score 1.00
• P02699 · AlphaFold monomer V2.0 prediction for rhodopsin (P02699) · a predicted model of the same protein · chain A against A, TM-score 0.99
• P08168 · AlphaFold monomer V2.0 prediction for S-arrestin (P08168) · a predicted model of the same protein · chain B against A, TM-score 0.55

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
• Every structure of UniProt P08168
• Elsewhere: RCSB PDB 4PXF · PDBe 4PXF · UniProt P02699 · UniProt P08168