Crystal structure of the ternary complex of peptidoglycan recognition protein, pgrp-S with hexanoic and tartaric acids at 2.67 a resolution.

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 20% strand (DSSP).

Ligands and binding sites

• 6NA · Hexanoic acid · ligand · chains C, D
• CL · Chloride ion · ion · chains B
• EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C, D
• TLA · L(+)-tartaric acid · additive · 3 copies · chains A, C, D
• ACT · Acetate ion · additive · chains C
• GOL · Glycerol · additive · chains C, D

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

Pockets

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

Interfaces

5 interfaces between chains.

• A–B · 705 Ų buried · 12 hydrogen bonds · protein-protein
• C–D · 556 Ų buried · 6 hydrogen bonds · protein-protein
• A–C · 350 Ų buried · 6 hydrogen bonds · protein-protein
• A–D · 82 Ų buried · 1 hydrogen bond · protein-protein
• B–D · 10 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

• 7XFY · Crystal structure of the ternary complex of Peptidoglycan recognition protein, PGRP-S… · the same entry in another collection · chain A against A, TM-score 1.00
• Q9GK12 · AlphaFold monomer V2.0 prediction for peptidoglycan recognition protein 1 (Q9GK12) · 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 Q9GK12
• Elsewhere: RCSB PDB 7XFY · PDBe 7XFY · UniProt Q9GK12