Crystal structure of the light-activated constitutively active N2C, M257Y,D282C rhodopsin mutant in complex with a peptide resembling the C-terminus of the galpha-protein subunit (gact)

Structure

x-ray diffraction · 2 distinct chains · 67% helix, 4% strand (DSSP).

Ligands and binding sites

• ACE · Acetyl group · ligand · chains A
• RET · Retinal · ligand · chains A
• PLM · Palmitic acid · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
• ACT · Acetate ion · additive · chains A
• BOG · octyl beta-D-glucopyranoside · 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.

Interfaces

1 interface between chains.

• A–B · 700 Ų buried · 5 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 4A4M · Crystal structure of the light-activated constitutively active N2C, M257Y,D282C rhodopsin… · 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
• P0C7Q4 · 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 0.70

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 P0C7Q4
• Elsewhere: RCSB PDB 4A4M · PDBe 4A4M · UniProt P02699 · UniProt P0C7Q4