SMTL ID : 8akl.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

monomer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: Q.201, V.204, K.208, A.226, W.247 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.201, A:Q.201, A:Q.201, A:K.208 Water bridges: A:W.247

1 x O2F: (2S,3R,4R)-4-[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl-3-methyl-2-[(2S,3R)-3-oxidanyl-1-oxidanylidene-butan-2-yl]-3,4-dihydro-2H-pyrrole-5-carboxylic acid(Covalent)

O2F.2: 17 residues within 4Å: Chain A: C.65, S.66, K.69, W.101, S.126, N.128, Q.162, N.166, T.212, R.216, K.230, T.231, G.232, T.233, C.234, G.235, H.269 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.101 Hydrogen bonds: A:S.66, A:N.128, A:T.212, A:T.212, A:T.231, A:T.233 Water bridges: A:H.269, A:H.269 Salt bridges: A:K.230

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

SO4.3: 3 residues within 4Å: Chain A: S.270, E.271, A.272 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.271, A:A.272 SO4.4: 2 residues within 4Å: Chain A: P.222, A.223 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.223 Water bridges: A:A.219 SO4.5: 2 residues within 4Å: Chain A: T.249, G.250 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.250 Water bridges: A:P.248 SO4.6: 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

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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