Crystal structure of the 11-cis isomer of pharaonis halorhodopsin in the absence of halide ions

Structure

x-ray diffraction · 3 distinct chains · 33% helix, 63% strand (DSSP).

Ligands and binding sites

• BNG · nonyl beta-D-glucopyranoside · ligand · 7 copies · chains A, E, D, G, B, F
• RET · Retinal · ligand · 6 copies · chains A, E, B, F, D, G
• L3P · 2,3-di-O-phytanly-3-sn-glycero-1-phosphoryl-3'-sn-glycerol-1'-phosphate · ligand · 6 copies · chains A, E, D, G, B, F
• 22B · Bacterioruberin · ligand · chains A, B, E, F
• ILE · Isoleucine · ligand · chains A, D, E, G

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

Pockets

11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Interfaces

15 interfaces between chains.

• A–E · 5719 Ų buried · 1,909 hydrogen bonds · protein-protein
• D–G · 5718 Ų buried · 1,945 hydrogen bonds · protein-protein
• B–F · 5714 Ų buried · 1,906 hydrogen bonds · protein-protein
• A–G · 829 Ų buried · 6 hydrogen bonds · protein-protein
• A–D · 818 Ų buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 cofactor, 8 disulfide, 3 covalent (retinal Schiff base, disulfide, covalent ligand).

Compared structures

• 5B0W · Crystal structure of the 11-cis isomer of pharaonis halorhodopsin in the absence of… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

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• Every structure of UniProt Q3ITX1
• Elsewhere: RCSB PDB 5B0W · PDBe 5B0W · UniProt Q3ITX1