Crystal structure of the complex of peptidoglycan recognition protein, pgrp-S from camel with ethylene glycol at 1.83 a resolution

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 20% strand (DSSP).

Ligands and binding sites

• EDO · 1,2-ethanediol · additive · 2 copies · chains C, A, D
• TLA · L(+)-tartaric acid · additive · chains C, D
• GOL · Glycerol · additive · chains C, D

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

4 interfaces between chains.

• A–B · 662 Ų buried · 14 hydrogen bonds · protein-protein
• C–D · 522 Ų buried · 5 hydrogen bonds · protein-protein
• A–C · 372 Ų buried · 8 hydrogen bonds · protein-protein
• A–D · 19 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

• 5DWF · Crystal structure of the complex of Peptidoglycan recognition protein, PGRP-S from camel… · 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 5DWF · PDBe 5DWF · UniProt Q9GK12