Unexpected tricovalent binding mode of boronic acids within the active site of a penicillin binding protein

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 24% strand (DSSP).

Ligands and binding sites

• FP5 · Phenylacetamidomethyl boronic acid · ligand · 2 copies · chains B, C
• ACN · Acetone · ligand · 2 copies · chains B, C
• 33D · 3,3-dimethylbutan-1-ol · ligand · 2 copies · chains C, B
• MG · Magnesium ion · metal · 14 copies · chains A, B, D, C
• SO4 · Sulfate ion · ion · 18 copies · chains A, B, C, D
• MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains 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, 4 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• B–D · 450 Ų buried · 7 hydrogen bonds · protein-protein
• A–B · 386 Ų buried · 3 hydrogen bonds · protein-protein
• C–D · 134 Ų buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 covalent (covalent ligand).

Compared structures

• 3ZVW · Unexpected tricovalent binding mode of boronic acids within the active site of a… · the same entry in another collection · chain D against D, TM-score 1.00
• P39045 · AlphaFold monomer V2.0 prediction for D-alanyl-D-alanine carboxypeptidase (P39045) · 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 P39045
• Elsewhere: RCSB PDB 3ZVW · PDBe 3ZVW · UniProt P39045