SMTL ID : 7a61.1

Crystal structure of KPC-2 with hydrolyzed faropenem (ring-open form)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

monomer

Ligands

1 x R0B: (2~{R})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-5-butyl-2,3-dihydro-1,3-thiazole-4-carboxylic acid(Covalent)

R0B.1: 17 residues within 4Å: Chain A: C.65, S.66, K.69, W.101, S.126, N.128, Q.162, L.163, N.166, T.212, R.216, K.230, T.231, G.232, T.233, C.234, H.269 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.66, A:S.126, A:S.126, A:N.128, A:T.212, A:T.231, A:T.233 Water bridges: A:S.126, A:T.233 Salt bridges: A:R.216, A:K.230

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: Q.201, V.204, K.208, A.226, W.247 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.201, A:Q.201, A:Q.201, A:K.208 GOL.7: 9 residues within 4Å: Chain A: R.61, F.62, P.63, I.169, P.170, G.171, D.172, T.176, R.261 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:I.169, A:G.171, A:R.261 Water bridges: A:E.60, A:E.60, A:D.172, A:R.261, A:R.261, A:R.261

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 2 residues within 4Å: Chain A: P.222, A.223 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.223 SO4.4: 3 residues within 4Å: Chain A: S.270, E.271, A.272 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.269, A:E.271, A:A.272 SO4.5: 3 residues within 4Å: Chain A: G.235, K.268, H.269 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.269 Water bridges: A:G.235, A:H.269 Salt bridges: A:H.269 SO4.6: 1 residues within 4Å: Chain A: R.57 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.57, A:R.57 Salt bridges: A:R.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lucic, A. et al., Faropenem reacts with serine and metallo-beta-lactamases to give multiple products. Eur.J.Med.Chem. (2021)

Release Date

2021-02-24

Peptides

Carbapenem-hydrolyzing beta-lactamase KPC: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Carbapenem-hydrolyzing beta-lactamase KPC

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