Structural basis of recognition of pathogen-associated molecular patterns and inhibition of proinflammatory cytokines by camel peptidoglycan recognition protein

Structure

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

Ligands and binding sites

• LP5 · (R)-((2R,3S,4R,5R,6R)-3-hydroxy-2-(hydroxymethyl)-5-((R)-3-hydroxytetradecanamido)-6-(phosphonooxy) tetrahydro-2H-pyran-4-yl) 3-hydroxytetradecanoate · ligand · chains A, 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

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

Interfaces

5 interfaces between chains.

• A–B · 859 Ų buried · 16 hydrogen bonds · protein-protein
• C–D · 529 Ų buried · 7 hydrogen bonds · protein-protein
• A–C · 328 Ų buried · 8 hydrogen bonds · protein-protein
• B–D · 123 Ų buried · 1 hydrogen bond · protein-protein
• A–D · 84 Ų buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

• 3RT4 · Structural Basis of Recognition of Pathogen-associated Molecular Patterns and Inhibition… · 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 3RT4 · PDBe 3RT4 · UniProt Q9GK12