Bacteriorhodopsin, 740 fs state, real-space refined against 15% extrapolated structure factors

Structure

x-ray diffraction · 1 distinct chain · 74% helix, 5% strand (DSSP).

Ligands and binding sites

• L2P · 2,3-di-phytanyl-glycerol · ligand · 3 copies · chains A
• RET · Retinal · ligand · chains A
• TRD · Tridecane · ligand · chains A
• D10 · Decane · ligand · chains A
• HP6 · Heptane · ligand · chains A
• MYS · Pentadecane · ligand · chains A
• C14 · Tetradecane · ligand · chains A
• OCT · N-octane · additive · 3 copies · chains A
• UND · Undecane · additive · 2 copies · chains A
• DD9 · nonane · additive · chains A

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

Pockets

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

Modifications

Observed in the structure: 1 cofactor (retinal Schiff base).

Compared structures

• 6GAI · Bacteriorhodopsin, 740 fs state, real-space refined against 15% extrapolated structure… · the same entry in another collection · chain A against A, TM-score 1.00
• P02945 · AlphaFold monomer V2.0 prediction for bacteriorhodopsin (P02945) · a predicted model of the same protein · 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 P02945
• Elsewhere: RCSB PDB 6GAI · PDBe 6GAI · UniProt P02945