Structure of the M intermediate of bacteriorhodopsin trapped at 100K

Structure

x-ray diffraction · 1 distinct chain · 74% helix, 4% strand (DSSP).

Ligands and binding sites

• L2P · 2,3-di-phytanyl-glycerol · ligand · 2 copies · chains A
• RET · Retinal · ligand · chains A
• L1P · 3-phosphoryl-[1,2-di-phytanyl]glycerol · ligand · chains A
• L3P · 2,3-di-O-phytanly-3-sn-glycero-1-phosphoryl-3'-sn-glycerol-1'-phosphate · ligand · chains A
• L4P · 3-[glycerolylphosphonyl]-[1,2-di-phytanyl]glycerol · ligand · chains A
• GLC · alpha-D-glucopyranose · sugar · chains A
• MAN · alpha-D-mannopyranose · sugar · chains A
• GAL · beta-D-galactopyranose · sugar · chains A

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

Pockets

1 pocket 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

• 1DZE · Structure of the M Intermediate of Bacteriorhodopsin trapped at 100K · 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 0.99

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 1DZE · PDBe 1DZE · UniProt P02945