Crystal structure of the complex of peptidoglycan recognition protein with methyloxane-2,3,4,5-tetrol at 2.9 a resolution

Structure

x-ray diffraction · 1 distinct chain · 29% helix, 20% strand (DSSP).

Ligands and binding sites

• RAM · alpha-L-rhamnopyranose · sugar · 2 copies · chains A, B
• TLA · L(+)-tartaric acid · additive · chains C, D

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

Pockets

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

Interfaces

5 interfaces between chains.

• A–B · 762 Ų buried · 9 hydrogen bonds · protein-protein
• C–D · 514 Ų buried · 4 hydrogen bonds · protein-protein
• A–C · 367 Ų buried · 6 hydrogen bonds · protein-protein
• B–D · 101 Ų buried · 0 hydrogen bonds · protein-protein
• A–D · 85 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

• 3CG9 · Crystal structure of the complex of peptidoglycan recognition protein 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 3CG9 · PDBe 3CG9 · UniProt Q9GK12