Crystal structure of the complex of peptidoglycan recognition protein (pgrp-S) with dipeptide L-ala D-glu at 2.7 a resolution

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 19% strand (DSSP).

Ligands and binding sites

• SRT · S,R meso-tartaric acid · ligand · chains C, D
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains B
• GOL · Glycerol · additive · 5 copies · chains A, D, C
• EDO · 1,2-ethanediol · additive · chains A
• PEG · Di(hydroxyethyl)ether · additive · chains B, D

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

Pockets

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

Interfaces

5 interfaces between chains.

• A–B · 793 Ų buried · 15 hydrogen bonds · protein-protein
• C–D · 607 Ų buried · 5 hydrogen bonds · protein-protein
• A–C · 404 Ų buried · 8 hydrogen bonds · protein-protein
• B–D · 91 Ų buried · 0 hydrogen bonds · protein-protein
• A–D · 84 Ų buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 12 disulfide, 1 d-amino (disulfide, D-amino acid).

Compared structures

• 3QV4 · Crystal structure of the complex of peptidoglycan recognition protein (PGRP-S) with… · 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 0.97

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 3QV4 · PDBe 3QV4 · UniProt Q9GK12