Crystal structure of ampc from E. COLI with taniborbactam (vnrx-5133)

Structure

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

Ligands and binding sites

• KJK · (3~{R})-3-[2-[4-(2-azanylethylamino) cyclohexyl]ethanoylamino]-2-oxidanyl-3,4-dihydro-1,2-benzoxaborinine-8-carboxylic acid · ligand · chains A
• K9K · (10AR)-2-(((1R,4R)-4-((2-aminoethyl)amino)cyclohexyl) methyl)-6-carboxy-4-hydroxy-4,10A-dihydro-10H-benzo[5, 6][1,2]oxaborinino[2,3-b][1,4,2]oxazaborol-4-uide · ligand · chains A
• ZN · Zinc ion · metal · 2 copies · chains A
• NA · Sodium ion · metal · chains A
• CL · Chloride ion · ion · 3 copies · chains A
• EDO · 1,2-ethanediol · additive · 3 copies · chains A
• MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
• PEG · Di(hydroxyethyl)ether · additive · chains A

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

Pockets

1 pocket 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

• 6YEN · Crystal structure of AmpC from E. coli with Taniborbactam (VNRX-5133) · 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 6YEN · PDBe 6YEN · UniProt P00811