SMTL ID : 8akk.1

Acyl-enzyme complex of imipenem bound to deacylation mutant KPC-2 (E166Q)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.36 Å

Oligo State

monomer

Ligands

1 x ID1: Imipenem(Covalent)

ID1.1: 16 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, K.230, T.231, G.232, T.233, C.234 Ligands: HIW.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:S.66, A:W.101 Hydrogen bonds: A:S.66, A:N.128, A:T.212, A:T.231, A:T.233 Water bridges: A:T.233, A:T.233 Salt bridges: A:K.230

1 x HIW: (2R,4S)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-4-[(2-{[(Z)-iminomethyl]amino}ethyl)sulfanyl]-3,4-dihydro-2H-pyrrole-5-ca rboxylic acid(Covalent)

HIW.2: 18 residues within 4Å: Chain A: C.65, S.66, K.69, W.101, S.126, N.128, Q.162, L.163, N.166, T.211, T.212, R.216, K.230, T.231, G.232, T.233, C.234 Ligands: ID1.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:S.66 Hydrogen bonds: A:S.66, A:S.126, A:N.128, A:T.211, 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

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

SO4.3: 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 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: 2 residues within 4Å: Chain A: P.222, A.223 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.223

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 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:K.208 Water bridges: A:T.190, A:D.205 GOL.7: 10 residues within 4Å: Chain A: R.61, F.62, P.63, A.168, I.169, P.170, G.171, D.172, T.176, R.261 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.169, A:G.171, A:R.261 Water bridges: A:D.172

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tooke, C.L. et al., Tautomer-Specific Deacylation and Omega-Loop Flexibility Explain the Carbapenem-Hydrolyzing Broad-Spectrum Activity of the KPC-2 beta-Lactamase. J.Am.Chem.Soc. (2023)

Release Date

2023-03-08

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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