SMTL ID : 6td0.1

Crystal structure of vaborbactam bound to KPC-2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 0.99 Å

Oligo State

monomer

Ligands

1 x 4D6: Vaborbactam(Covalent)

4D6.1: 17 residues within 4Å: Chain A: C.65, S.66, K.69, W.101, S.126, N.128, E.162, L.163, N.166, T.212, R.216, K.230, T.231, G.232, T.233, C.234, G.235 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:W.101 Hydrogen bonds: A:S.66, A:S.66, A:S.126, A:N.128, A:N.166, A:N.166, A:T.212, A:T.231, A:T.233, A:T.233, A:T.233 Water bridges: A:K.69, A:K.69 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.201, A:K.208 Water bridges: A:Q.201 GOL.3: 9 residues within 4Å: Chain A: R.61, F.62, P.63, I.169, P.170, G.171, D.172, T.176, R.261 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.171, A:R.261 Water bridges: A:D.172

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

SO4.4: 3 residues within 4Å: Chain A: S.270, E.271, A.272 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.269, A:S.270, A:E.271, A:A.272 SO4.5: 3 residues within 4Å: Chain A: I.169, Y.237, K.265 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.237 Salt bridges: A:K.265 SO4.6: 1 residues within 4Å: Chain A: R.57 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.57 Salt bridges: A:R.57 SO4.7: 1 residues within 4Å: Chain A: D.88 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.88 SO4.8: 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:V.236 Salt bridges: A:K.268, A:H.269

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tooke, C.L. et al., Cyclic boronates as versatile scaffolds for KPC-2 beta-lactamase inhibition. Rsc Med Chem (2020)

Release Date

2020-01-22

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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