Crystal structure of the constitutively active E113Q,D2C,D282C rhodopsin mutant with bound galphact peptide.

Structure

x-ray diffraction · 2 distinct chains · 69% helix, 4% strand (DSSP).

Ligands and binding sites

• PLM · Palmitic acid · ligand · 2 copies · chains A
• ACE · Acetyl group · ligand · chains A
• PEF · Di-palmitoyl-3-sn-phosphatidylethanolamine · ligand · chains A
• RET · Retinal · ligand · chains A
• LPP · 2-(hexadecanoyloxy)-1-[(phosphonooxy)methyl]ethyl hexadecanoate · 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 · chains A
• ACT · Acetate ion · additive · 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.

Interfaces

1 interface between chains.

• A–B · 703 Ų buried · 4 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 2X72 · Crystal structure of the constitutively active E113Q,D2C,D282C rhodopsin mutant with… · 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
• P04695 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(T) subunit… · a predicted model of the same protein · chain B against A, TM-score 0.76

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 P04695
• Elsewhere: RCSB PDB 2X72 · PDBe 2X72 · UniProt P02699 · UniProt P04695