Crystal structure of penicillin-binding protein 6 (PBP6) from E. COLI in complex with a substrate fragment

Structure

x-ray diffraction · 5 distinct chains · 30% helix, 31% strand (DSSP).

Ligands and binding sites

• AMV · methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside · ligand · chains D, L
• GLC · alpha-D-glucopyranose · sugar · chains C
• FRU · beta-D-fructofuranose · sugar · chains C
• SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D

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

Pockets

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

Interfaces

7 interfaces between chains.

• C–D · 877 Ų buried · 7 hydrogen bonds · protein-protein
• A–B · 868 Ų buried · 7 hydrogen bonds · protein-protein
• C–L · 379 Ų buried · 12 hydrogen bonds · protein-protein
• B–C · 364 Ų buried · 3 hydrogen bonds · protein-protein
• D–L · 145 Ų buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 2 d-amino, 1 covalent, 1 modified (D-amino acid, covalent ligand, nonstandard).

Compared structures

• 3ITB · Crystal structure of Penicillin-Binding Protein 6 (PBP6) from E. coli in complex with a… · the same entry in another collection · chain L against L, TM-score 1.00
• P08506 · AlphaFold monomer V2.0 prediction for D-alanyl-D-alanine carboxypeptidase dacc (P08506) · a predicted model of the same protein · chain C against A, TM-score 0.99

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 P08506
• Elsewhere: RCSB PDB 3ITB · PDBe 3ITB · UniProt P08506