SMTL ID : 6z23.1

Acylenzyme complex of cefotaxime bound to deacylation mutant KPC-2 (E166Q)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.31 Å

Oligo State

monomer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 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 GOL.2: 9 residues within 4Å: Chain A: N.24, V.26, A.27, E.28, F.30, V.54, S.55, Y.56, G.284 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.24, A:V.26 Water bridges: A:N.24, A:F.30

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

SO4.3: 4 residues within 4Å: Chain A: H.269, 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 SO4.4: 1 residues within 4Å: Chain A: R.180 4 PLIP interactions: 4 interactions with chain A Water bridges: A:T.23, A:T.23, A:R.180 Salt bridges: A:R.180 SO4.5: 1 residues within 4Å: Chain A: R.57 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.57 SO4.6: 3 residues within 4Å: Chain A: R.160, I.169, R.174 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.160 Water bridges: A:S.167, A:S.167, A:R.174, A:R.174, A:R.174 Salt bridges: A:R.174 SO4.7: 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

1 x CEF: CEFOTAXIME, C3' cleaved, open, bound form(Covalent)

CEF.8: 20 residues within 4Å: Chain A: C.65, S.66, K.69, W.101, Y.125, S.126, N.128, Q.162, L.163, N.166, T.212, R.216, K.230, T.231, G.232, T.233, C.234, G.235, K.268, H.269 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.66, A:S.126, A:N.128, A:T.231, A:T.233, A:T.233, A:T.233, A:T.233 Salt bridges: A:R.216, A:K.230

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tooke, C.L. et al., Natural variants modify Klebsiella pneumoniae carbapenemase (KPC) acyl-enzyme conformational dynamics to extend antibiotic resistance. J.Biol.Chem. (2020)

Release Date

2020-12-23

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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