Catalytic domain of lyta, the major autolysin of streptococcus pneumoniae, (C60A, H133A, C136A mutant) complexed with peptidoglycan fragment

Structure

x-ray diffraction · 3 distinct chains · 35% helix, 15% strand (DSSP).

Ligands and binding sites

• AMV · methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside · ligand · 2 copies · chains A, E, C
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A

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

Interfaces

2 interfaces between chains.

• A–C · 396 Ų buried · 9 hydrogen bonds · protein-protein
• A–E · 97 Ų buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 3 d-amino, 2 covalent (D-amino acid, covalent ligand).

Compared structures

• 5CTV · Catalytic domain of LytA, the major autolysin of Streptococcus pneumoniae, (C60A, H133A… · the same entry in another collection · chain A against A, TM-score 1.00
• P06653 · AlphaFold monomer V2.0 prediction for autolysin (P06653) · 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 P06653
• Elsewhere: RCSB PDB 5CTV · PDBe 5CTV · UniProt P06653