SMTL ID : 6ypd.1

Crystal structure of AmpC from E. coli with Cyclic Boronate 3 (CB3 / APC308)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x KL8: (3~{S})-2,2-bis(oxidanyl)-3-(phenylmethylsulfanyl)-3,4-dihydro-1,2-benzoxaborinin-2-ium-8-carboxylic acid(Covalent)

KL8.1: 16 residues within 4Å: Chain A: G.60, S.61, K.64, Q.117, Y.147, N.149, V.208, Y.218, N.286, L.290, K.312, T.313, G.314, A.315, T.316, N.343 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.147, A:V.208, A:L.290, A:T.316 Hydrogen bonds: A:S.61, A:Y.147, A:Y.147, A:A.315, A:A.315, A:N.343 Water bridges: A:K.312, A:T.313, A:T.313 Salt bridges: A:K.312 pi-Stacking: A:Y.218

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 3 residues within 4Å: Chain A: W.90, L.128, A.157 No protein-ligand interaction detected (PLIP) PEG.5: 5 residues within 4Å: Chain A: Y.37, F.38, T.39, T.52, Q.53 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.37, A:T.39, A:Q.53

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 5 residues within 4Å: Chain A: D.278, I.281, D.348, Q.352 Ligands: EDO.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.352 Salt bridges: A:D.278

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 1 residues within 4Å: Ligands: DMS.3 No protein-ligand interaction detected (PLIP) EDO.6: 3 residues within 4Å: Chain A: N.340, Y.341, P.342 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.20, A:K.339

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

CL.7: 3 residues within 4Å: Chain A: H.10, R.11 Ligands: ZN.8 Ligand excluded by PLIP

1 x ZN: ZINC ION(Non-covalent)

ZN.8: 2 residues within 4Å: Chain A: H.10 Ligands: CL.7 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.10

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
A

Beta-lactamase

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