Bacterial membrane enzyme structure by the in meso method at 1.9 a resolution

Structure

x-ray diffraction · 2 distinct chains · 57% helix, 13% strand (DSSP).

Ligands and binding sites

• 5BV · (2R,3R)-3-(glycyloxy)-2-methylnonanoic acid · ligand · chains A, B
• ZN · Zinc ion · metal · chains A
• 7PE · 2-(2-(2-(2-(2-(2-ethoxyethoxy)ethoxy)ethoxy)ethoxy) ethoxy)ethanol · additive · 10 copies · chains A, B
• OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 6 copies · chains A, B
• GOL · Glycerol · additive · 5 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, 0 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 429 Ų buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 modified, 2 covalent (nonstandard, covalent ligand).

Compared structures

• 6RYO · Bacterial membrane enzyme structure by the in meso method at 1.9 A resolution · the same entry in another collection · chain A against A, TM-score 1.00
• Q6GHN9 · AlphaFold monomer V2.0 prediction for lipoprotein signal peptidase (Q6GHN9) · a predicted model of the same protein · chain A against A, TM-score 0.92

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 Q6GHN9
• Elsewhere: RCSB PDB 6RYO · PDBe 6RYO · UniProt Q6GHN9