Crystal structure of the complex of peptidoglycan recognition protein (pgrp-S) and lipoteichoic acid at 2.1 a resolution

Structure

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

Ligands and binding sites

• LTC · (2S)-1-({3-O-[2-(acetylamino)-4-amino-2,4,6-trideoxy-beta-D-galactopyranosyl]-alpha-D-glucopyranosyl}oxy)-3-(heptanoyloxy)propan-2-yl (7Z)-pentadec-7-enoate · ligand · chains A, C, D
• GOL · Glycerol · additive · chains C, D
• TLA · L(+)-tartaric acid · additive · chains C, D

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

Pockets

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

Interfaces

5 interfaces between chains.

• A–B · 793 Ų buried · 16 hydrogen bonds · protein-protein
• C–D · 526 Ų buried · 5 hydrogen bonds · protein-protein
• A–C · 343 Ų buried · 9 hydrogen bonds · protein-protein
• B–D · 102 Ų buried · 1 hydrogen bond · protein-protein
• A–D · 71 Ų buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 11 disulfide (disulfide).

Compared structures

• 3O4K · Crystal structure of the complex of peptidoglycan recognition protein (PGRP-S) and… · the same entry in another collection · chain C against C, 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 0.97

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 3O4K · PDBe 3O4K · UniProt Q9GK12