SMTL ID : 8peb.1

OXA-48_Q5. Epistasis Arises from Shifting the Rate-Limiting Step during Enzyme Evolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.17 Å

Oligo State

homo-dimer

Ligands

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 7 residues within 4Å: Chain A: Q.170, L.173, R.183 Chain B: Q.170, L.173, R.183 Ligands: CL.7 Ligand excluded by PLIP CL.2: 5 residues within 4Å: Chain A: T.174, A.184, K.185, T.186, W.199 Ligand excluded by PLIP CL.3: 6 residues within 4Å: Chain A: L.44, D.125, S.127, G.128, V.130, R.140 Ligand excluded by PLIP CL.7: 7 residues within 4Å: Chain A: Q.170, L.173, R.183 Chain B: Q.170, L.173, R.183 Ligands: CL.1 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain B: T.174, A.184, K.185, T.186, W.199 Ligand excluded by PLIP CL.9: 6 residues within 4Å: Chain B: L.44, D.125, S.127, G.128, V.130, R.140 Ligand excluded by PLIP

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

SO4.4: 8 residues within 4Å: Chain A: A.176, N.177, G.178, I.181 Chain B: K.93, L.173, T.174 Ligands: PEG.5 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.177, A:N.177, A:G.178 Water bridges: A:N.177, B:K.93, B:L.173 Salt bridges: B:K.93 SO4.10: 8 residues within 4Å: Chain A: K.93, L.173, T.174 Chain B: A.176, N.177, G.178, I.181 Ligands: PEG.11 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Water bridges: A:K.93, A:L.173, B:N.177 Salt bridges: A:K.93 Hydrogen bonds: B:N.177, B:N.177

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 6 residues within 4Å: Chain A: N.177, G.178, D.179 Chain B: T.174, E.175 Ligands: SO4.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.178 PEG.11: 6 residues within 4Å: Chain A: T.174, E.175 Chain B: N.177, G.178, D.179 Ligands: SO4.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.178

2 x MLI: MALONATE ION(Non-functional Binders)

MLI.6: 10 residues within 4Å: Chain A: A.46, S.47, K.50, S.95, K.185, T.186, G.187, Y.188, L.224, R.227 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.47, A:S.47, A:S.47, A:S.95, A:Y.188 Water bridges: A:T.186, A:R.227, A:R.227 Salt bridges: A:K.50, A:K.185, A:R.227 MLI.12: 10 residues within 4Å: Chain B: A.46, S.47, K.50, S.95, K.185, T.186, G.187, Y.188, L.224, R.227 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.47, B:S.47, B:S.47, B:S.95, B:Y.188 Water bridges: B:T.186, B:R.227, B:R.227 Salt bridges: B:K.50, B:K.185, B:R.227

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Frohlich, C. et al., Epistasis arises from shifting the rate-limiting step during enzyme evolution of a beta-lactamase. Nat Catal (2024)

Release Date

2024-02-14

Peptides

Beta-lactamase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Beta-lactamase

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