SMTL ID : 6qwa.1

Crystal structure of KPC-3 complexed with relebactam (16 hour soak)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.06 Å

Oligo State

monomer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: S.270, E.271, A.272 Ligands: EOH.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.269, A:E.271, A:A.272 SO4.2: 10 residues within 4Å: Chain A: S.66, S.126, T.212, R.216, K.230, T.231, G.232, T.233 Ligands: MK7.5, JJT.6 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.126, A:T.212, A:R.216, A:T.231, A:T.231, A:T.233 Water bridges: A:T.233 Salt bridges: A:K.230

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: Q.201, V.204, K.208, A.226, W.247 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.201, A:Q.201, A:K.208

1 x EOH: ETHANOL(Non-functional Binders)

EOH.4: 5 residues within 4Å: Chain A: K.268, Y.269, S.270, E.271 Ligands: SO4.1 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.269 Hydrogen bonds: A:Y.269

1 x MK7: (2S,5R)-1-formyl-N-(piperidin-4-yl)-5-[(sulfooxy)amino]piperidine-2-carboxamide(Covalent)

MK7.5: 20 residues within 4Å: Chain A: C.65, S.66, K.69, P.100, W.101, Y.125, S.126, N.128, E.162, L.163, N.166, T.212, K.230, T.231, G.232, T.233, C.234, G.235 Ligands: SO4.2, JJT.6 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:W.101, A:L.163 Hydrogen bonds: A:S.66, A:S.126, A:N.128, A:N.166, A:T.212, A:T.231, A:T.231, A:T.233, A:T.233, A:T.233 Water bridges: A:K.69, A:K.69 Salt bridges: A:K.230

1 x JJT: (2~{S})-5-azanylidene-2-(piperidin-4-ylcarbamoyl)piperidine-1-carboxylic acid(Covalent)

JJT.6: 17 residues within 4Å: Chain A: C.65, S.66, K.69, P.100, W.101, Y.125, S.126, N.128, E.162, L.163, N.166, G.232, T.233, C.234, G.235 Ligands: SO4.2, MK7.5 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.101, A:L.163 Hydrogen bonds: A:S.66, A:S.126, A:N.128, A:N.166, A:T.233, A:T.233 Water bridges: A:K.69, A:K.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tooke, C.L. et al., Molecular Basis of Class A beta-Lactamase Inhibition by Relebactam. Antimicrob.Agents Chemother. (2019)

Release Date

2019-08-21

Peptides

Beta-lactamase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-lactamase

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