Serial femtosecond crystallography (sfx) of ground state bacteriorhodopsin crystallized from bicelles in complex with HAD16 determined using 7-kev X-ray free electron laser (xfel) at sacla

Structure

x-ray diffraction · 1 distinct chain · 79% helix, 5% strand (DSSP).

Ligands and binding sites

• HP6 · Heptane · ligand · 5 copies · chains A
• D12 · Dodecane · ligand · 3 copies · chains A
• R16 · Hexadecane · ligand · 3 copies · chains A
• D10 · Decane · ligand · 2 copies · chains A
• RET · Retinal · ligand · chains A
• 7YH · 2-[[(2R)-2-(3-bromanyl-5-iodanyl-phenyl)carbonyloxy-3-tetradecanoyloxy-propoxy]-oxidanyl-phosphoryl]oxyethyl-trimethyl-azanium · ligand · chains A
• CPS · 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate · ligand · chains A
• IOD · Iodide ion · ion · chains A
• OCT · N-octane · 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

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

• 7VSO · 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 7VSO · PDBe 7VSO · UniProt P02945