Structure of ground-state bovine rhodospin in a hexagonal crystal form

Structure

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

Ligands and binding sites

• PLM · Palmitic acid · ligand · 2 copies · chains A
• ACE · Acetyl group · ligand · chains A
• RET · Retinal · ligand · chains A
• PEF · Di-palmitoyl-3-sn-phosphatidylethanolamine · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
• BMA · beta-D-mannopyranose · sugar · 2 copies
• ZN · Zinc ion · metal · chains A
• C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 6 copies · chains A
• LDA · Lauryl dimethylamine-N-oxide · additive · chains A

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

Pockets

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

Modifications

Observed in the structure: 2 glycan, 2 lipid, 1 cofactor, 1 covalent, 1 disulfide (N-glycosylation, palmitoylation, retinal Schiff base, covalent ligand, disulfide).

Compared structures

• 3C9L · Structure of ground-state bovine rhodospin in a hexagonal crystal form · 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 0.91

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 3C9L · PDBe 3C9L · UniProt P02699