SMTL ID : 8akj.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: I.169, Y.237, K.265 Chain B: I.169, Y.237, K.265 Ligands: SO4.8 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Y.237, A:Y.237 Water bridges: B:K.265, B:K.265, A:K.265, A:K.265 Salt bridges: B:K.265, A:K.265 SO4.2: 3 residues within 4Å: Chain A: R.160, I.169, R.174 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.160 Water bridges: A:S.167, A:S.167, A:R.174, A:R.174 Salt bridges: A:R.174 SO4.3: 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 SO4.8: 7 residues within 4Å: Chain A: I.169, Y.237, K.265 Chain B: I.169, Y.237, K.265 Ligands: SO4.1 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Y.237, A:Y.237 Water bridges: B:K.265, B:K.265, A:K.265, A:K.265 Salt bridges: B:K.265, A:K.265 SO4.9: 3 residues within 4Å: Chain B: R.160, I.169, R.174 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.160 Water bridges: B:S.167, B:S.167, B:R.174, B:R.174 Salt bridges: B:R.174 SO4.10: 2 residues within 4Å: Chain B: T.249, G.250 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.250 Water bridges: B:P.248

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: R.61, F.62, P.63, I.169, P.170, G.171, D.172, T.176, R.261 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:I.169, A:G.171, A:R.261, A:R.261 Water bridges: A:G.171, A:D.172 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:Q.201, A:Q.201, A:K.208 GOL.7: 5 residues within 4Å: Chain A: I.169, D.172, R.174 Chain B: K.265, D.266 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Water bridges: B:D.266, A:G.171, A:A.173, A:A.173, A:R.174 GOL.11: 9 residues within 4Å: Chain B: R.61, F.62, P.63, I.169, P.170, G.171, D.172, T.176, R.261 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:I.169, B:G.171, B:R.261, B:R.261 Water bridges: B:G.171, B:D.172 GOL.13: 5 residues within 4Å: Chain B: Q.201, V.204, K.208, A.226, W.247 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.201, B:Q.201, B:Q.201, B:K.208 GOL.14: 5 residues within 4Å: Chain A: K.265, D.266 Chain B: I.169, D.172, R.174 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Water bridges: B:G.171, B:A.173, B:A.173, B:R.174, A:D.266

2 x CEO: 5-METHYLENE-2-[2-OXO-1-(2-THIOPHEN-2-YL-ACETYLAMINO)-ETHYL]-5,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID(Covalent)

CEO.5: 16 residues within 4Å: Chain A: C.65, S.66, K.69, W.101, S.126, N.128, L.163, N.166, T.212, R.216, K.230, T.231, G.232, T.233, C.234, G.235 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.66, A:S.126, A:N.128, A:N.166, A:T.231, A:T.233, A:T.233, A:T.233 Salt bridges: A:R.216, A:K.230 CEO.12: 16 residues within 4Å: Chain B: C.65, S.66, K.69, W.101, S.126, N.128, L.163, N.166, T.212, R.216, K.230, T.231, G.232, T.233, C.234, G.235 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.66, B:S.126, B:N.128, B:N.166, B:T.231, B:T.233, B:T.233, B:T.233 Salt bridges: B:R.216, B:K.230

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Carbapenem-hydrolyzing beta-lactamase KPC

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