SMTL ID : 6yeo.4 (3 other biounits)

Crystal structure of AmpC from E. coli with cyclic boronate 2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

monomer

Ligands

1 x OK3: (4~{R})-4-[[4-(aminomethyl)phenyl]carbonylamino]-3,3-bis(oxidanyl)-2-oxa-3-boranuidabicyclo[4.4.0]deca-1(10),6,8-triene-10-carboxylic acid(Covalent)

OK3.1: 14 residues within 4Å: Chain A: G.60, S.61, K.64, Y.147, N.149, Y.218, N.286, L.290, T.313, G.314, A.315, T.316, G.317, N.343 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.147, A:L.290 Hydrogen bonds: A:S.61, A:Y.147, A:N.149, A:R.201, A:N.286, A:T.313, A:A.315, A:A.315, A:A.315, A:N.343 Water bridges: A:N.286, A:R.346 Salt bridges: A:K.312

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 4 residues within 4Å: Chain A: P.137, A.138, W.139, A.140 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.138

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.3: 9 residues within 4Å: Chain A: I.75, K.81, L.82, S.83, L.251, S.254, Y.256, P.301, P.303 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.82, A:S.83, A:S.254 Water bridges: A:S.83

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 1 residues within 4Å: Chain A: Q.53 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lang, P.A. et al., Bicyclic Boronates as Potent Inhibitors of AmpC, the Class C beta-Lactamase from Escherichia coli . Biomolecules (2020)

Release Date

2020-06-24

Peptides

Beta-lactamase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

Beta-lactamase

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