Crystal structure of mammalian peptidoglycan recognition protein pgrp- S with paranitrophenyl palmitate and N-acetyl glucosamine at 2.09 a resolution

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 19% strand (DSSP).

Ligands and binding sites

• PNR · 4-nitrophenyl hexadecanoate · ligand · 2 copies · chains A, B, D, C
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains 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 · 686 Ų buried · 11 hydrogen bonds · protein-protein
• C–D · 540 Ų buried · 5 hydrogen bonds · protein-protein
• A–C · 357 Ų buried · 7 hydrogen bonds · protein-protein
• A–D · 62 Ų buried · 0 hydrogen bonds · protein-protein
• B–D · 49 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

• 4Q8S · Crystal structure of mammalian 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 0.98

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 4Q8S · PDBe 4Q8S · UniProt Q9GK12