M intermediate structure of the wild type bacteriorhodopsin in combination with the ground state structure

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 42% strand (DSSP).

Ligands and binding sites

• TRD · Tridecane · ligand · 6 copies · chains A, B
• RET · Retinal · ligand · 2 copies · chains A, B
• OCT · N-octane · additive · 16 copies · chains A, B
• HEX · Hexane · additive · 12 copies · chains A, B
• UND · Undecane · additive · 8 copies · chains A, B

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.

Interfaces

1 interface between chains.

• A–B · 5746 Ų buried · 1,773 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 cofactor, 1 covalent (retinal Schiff base, covalent ligand).

Compared structures

• 1CWQ · M intermediate structure of the wild type bacteriorhodopsin in combination with the… · 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 0.94

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 1CWQ · PDBe 1CWQ · UniProt P02945