Crystal structure of the C-terminal peptidoglycan binding domain of oprf (PA1777) from pseudomonas aeruginosa

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 26% strand (DSSP).

Ligands and binding sites

• 7QA · (2R,6S)-2-amino-6-(carboxyamino)-7-{[(1R)-1-carboxyethyl]amino}-7-oxoheptanoic acid · ligand · 4 copies · chains A, B, C, D
• SO4 · Sulfate ion · ion · 11 copies · chains B, C, D, A
• CL · Chloride ion · ion · 3 copies · chains A, B, D
• ACT · Acetate ion · additive · 2 copies · chains A, B

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

Pockets

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

Interfaces

6 interfaces between chains.

• C–D · 1346 Ų buried · 13 hydrogen bonds · protein-protein
• A–B · 1196 Ų buried · 10 hydrogen bonds · protein-protein
• B–C · 974 Ų buried · 19 hydrogen bonds · protein-protein
• A–D · 967 Ų buried · 20 hydrogen bonds · protein-protein
• A–C · 188 Ų buried · 2 hydrogen bonds · protein-protein

Compared structures

• 5U1H · Crystal structure of the C-terminal peptidoglycan binding domain of OprF (PA1777) from… · the same entry in another collection · chain D against D, TM-score 1.00
• P13794 · AlphaFold monomer V2.0 prediction for outer membrane porin F (P13794) · a predicted model of the same protein · chain A against A, TM-score 0.93

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 P13794
• Elsewhere: RCSB PDB 5U1H · PDBe 5U1H · UniProt P13794