Crystal structure of tracheal cytotoxin (tct) bound to the ectodomain complex of peptidoglycan recognition proteins lca (pgrp-lca) and lcx (pgrp-lcx)

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 20% strand (DSSP).

Ligands and binding sites

• HSQ · 2-acetylamino-2-deoxy-alpha-L-idopyranose · ligand · chains A
• MLD · Glcnac(beta1-4)-murnac(1,6-anhydro)-L-ala-gamma-D-glu-meso-A2PM-D-ala · ligand · chains A, X
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
• SO4 · Sulfate ion · ion · 2 copies · chains A, X
• CIT · Citric acid · additive · chains X

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

1 interface between chains.

• A–X · 603 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide, 1 covalent, 1 glycan, 1 modified (disulfide, covalent ligand, N-glycosylation, oxidation).

Compared structures

• 2F2L · Crystal structure of tracheal cytotoxin (TCT) bound to the ectodomain complex of… · the same entry in another collection · chain A against A, TM-score 1.00
• Q9GNK5 · AlphaFold monomer V2.0 prediction for peptidoglycan-recognition protein lc (Q9GNK5) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 Q9GNK5
• Elsewhere: RCSB PDB 2F2L · PDBe 2F2L · UniProt Q9GNK5