Serial femtosecond crystallography (sfx) of ground state bacteriorhodopsin crystallized from bicelles in complex with iodine- labeled detergent HAD13A determined using 7-kev X-ray free electron laser (xfel) at sacla

Structure

x-ray diffraction · 1 distinct chain · 78% helix, 5% strand (DSSP).

Ligands and binding sites

• D12 · Dodecane · ligand · 4 copies · chains A
• D10 · Decane · ligand · 3 copies · chains A
• HP6 · Heptane · ligand · 3 copies · chains A
• 4QL · 2,4,6-tris(iodanyl)-5-(octanoylamino)benzene-1,3-dicarboxylic acid · ligand · 2 copies · chains A
• RET · Retinal · ligand · chains A
• R16 · Hexadecane · ligand · chains A
• OCT · N-octane · additive · 2 copies · chains A
• DD9 · nonane · additive · 2 copies · 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

• 5B34 · Serial Femtosecond Crystallography (SFX) of Ground State Bacteriorhodopsin Crystallized… · 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 5B34 · PDBe 5B34 · UniProt P02945