Crystal structure of ampc from E. COLI with cyclic boronate 3 (CB3 / APC308)

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 23% strand (DSSP).

Ligands and binding sites

• KL8 · (3~{S})-2,2-bis(oxidanyl)-3-(phenylmethylsulfanyl)-3,4-dihydro-1,2-benzoxaborinin-2-ium-8-carboxylic acid · ligand · chains A
• ZN · Zinc ion · metal · chains A
• CL · Chloride ion · ion · chains A
• PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
• EDO · 1,2-ethanediol · additive · 2 copies · chains A
• DMS · Dimethyl sulfoxide · additive · chains A

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.

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

• 6YPD · Crystal structure of AmpC from E. coli with Cyclic Boronate 3 (CB3 / APC308) · the same entry in another collection · chain A against A, TM-score 1.00
• P00811 · AlphaFold monomer V2.0 prediction for beta-lactamase (P00811) · a predicted model of the same protein · chain A against A, TM-score 1.00
• 1L2S · X-ray crystal structure of AmpC beta-lactamase from E. coli in complex with a… · a predicted model of the same protein · chain A against B, TM-score 1.00
• 1L2S · X-ray crystal structure of ampc beta-lactamase from E. COLI in complex with a… · a predicted model of the same protein · chain A against B, 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 P00811
• Elsewhere: RCSB PDB 6YPD · PDBe 6YPD · UniProt P00811