SMTL ID : 7e9a.1 (3 other biounits)

Crystal structure of KPC-2 in complex with (S)-2-(1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborol-3-yl)acrylic acid (4a-(S))

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

1 x J00: 2-[(3S)-1-oxidanyl-3H-2,1-benzoxaborol-3-yl]prop-2-enoic acid(Covalent)

J00.1: 12 residues within 4Å: Chain A: C.44, S.45, W.80, S.105, N.107, T.191, R.195, T.210, G.211, T.212 Ligands: PEG.3, GOL.4 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.80, A:W.80 Hydrogen bonds: A:S.45, A:S.105, A:T.212, A:T.212, A:T.212 Water bridges: A:T.212, A:T.212 Salt bridges: A:R.195, A:K.209

1 x ACY: ACETIC ACID(Non-functional Binders)

ACY.2: 3 residues within 4Å: Chain A: S.249, E.250, A.251 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.250, A:A.251

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

PEG.3: 3 residues within 4Å: Chain A: W.80, T.191 Ligands: J00.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.191 Water bridges: A:T.210

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: T.212, C.213, G.214 Ligands: J00.1 No protein-ligand interaction detected (PLIP) GOL.5: 5 residues within 4Å: Chain A: A.54, R.58, L.117, G.122, F.126 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.58, A:G.122 GOL.6: 3 residues within 4Å: Chain A: E.38, E.39, R.40 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.38, A:R.40 Water bridges: A:R.40, A:R.240

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiao, Y.C. et al., Design and enantioselective synthesis of 3-( alpha-acrylic acid) benzoxaboroles to combat carbapenemase resistance. Chem.Commun.(Camb.) (2021)

Release Date

2021-08-04

Peptides

Beta-lactamase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-lactamase

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