SMTL ID : 7a63.1

Crystal structure of L1 with hydrolyzed faropenem (imine, ring-closed form)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

homo-tetramer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.86, H.88, H.91, H.162 Ligands: ZN.2, R3N.7 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.86, A:H.88, A:H.162, H2O.1 ZN.2: 7 residues within 4Å: Chain A: H.86, D.90, H.91, S.187, H.227 Ligands: ZN.1, R3N.7 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.90, A:H.91, A:H.227, H2O.1 ZN.3: 2 residues within 4Å: Chain A: D.30, H.31 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.31 ZN.8: 6 residues within 4Å: Chain B: H.86, H.88, H.91, H.162 Ligands: ZN.9, R3N.14 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.86, B:H.88, B:H.162, H2O.10 ZN.9: 7 residues within 4Å: Chain B: H.86, D.90, H.91, S.187, H.227 Ligands: ZN.8, R3N.14 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.90, B:H.91, B:H.227, H2O.10 ZN.10: 2 residues within 4Å: Chain B: D.30, H.31 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.31 ZN.15: 6 residues within 4Å: Chain C: H.86, H.88, H.91, H.162 Ligands: ZN.16, R3N.21 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.86, C:H.88, C:H.162, H2O.18 ZN.16: 7 residues within 4Å: Chain C: H.86, D.90, H.91, S.187, H.227 Ligands: ZN.15, R3N.21 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.90, C:H.91, C:H.227, H2O.18 ZN.17: 2 residues within 4Å: Chain C: D.30, H.31 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.31 ZN.22: 6 residues within 4Å: Chain D: H.86, H.88, H.91, H.162 Ligands: ZN.23, R3N.28 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.86, D:H.88, D:H.162, H2O.26 ZN.23: 7 residues within 4Å: Chain D: H.86, D.90, H.91, S.187, H.227 Ligands: ZN.22, R3N.28 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.90, D:H.91, D:H.227, H2O.26 ZN.24: 2 residues within 4Å: Chain D: D.30, H.31 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.31

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

SO4.4: 4 residues within 4Å: Chain A: R.139, V.146, I.147, T.148 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.148, A:T.148, A:T.148 Water bridges: A:R.139, A:R.139, A:R.139, A:R.139 Salt bridges: A:R.139 SO4.5: 5 residues within 4Å: Chain A: A.239, R.240, A.241, G.242, A.243 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.239, A:R.240, A:G.242, A:A.243 Water bridges: A:A.241, A:A.241 SO4.6: 2 residues within 4Å: Chain A: W.33, R.72 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.72 Salt bridges: A:R.72 SO4.11: 4 residues within 4Å: Chain B: R.139, V.146, I.147, T.148 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.148, B:T.148, B:T.148 Water bridges: B:R.139, B:R.139, B:R.139, B:R.139 Salt bridges: B:R.139 SO4.12: 5 residues within 4Å: Chain B: A.239, R.240, A.241, G.242, A.243 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.239, B:R.240, B:G.242, B:A.243 Water bridges: B:A.241, B:A.241 SO4.13: 2 residues within 4Å: Chain B: W.33, R.72 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.72 Salt bridges: B:R.72 SO4.18: 4 residues within 4Å: Chain C: R.139, V.146, I.147, T.148 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:T.148, C:T.148, C:T.148 Water bridges: C:R.139, C:R.139, C:R.139, C:R.139 Salt bridges: C:R.139 SO4.19: 5 residues within 4Å: Chain C: A.239, R.240, A.241, G.242, A.243 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:A.239, C:R.240, C:G.242, C:A.243 Water bridges: C:A.241, C:A.241 SO4.20: 2 residues within 4Å: Chain C: W.33, R.72 2 PLIP interactions: 2 interactions with chain C Water bridges: C:R.72 Salt bridges: C:R.72 SO4.25: 4 residues within 4Å: Chain D: R.139, V.146, I.147, T.148 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:T.148, D:T.148, D:T.148 Water bridges: D:R.139, D:R.139, D:R.139, D:R.139 Salt bridges: D:R.139 SO4.26: 5 residues within 4Å: Chain D: A.239, R.240, A.241, G.242, A.243 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:A.239, D:R.240, D:G.242, D:A.243 Water bridges: D:A.241, D:A.241 SO4.27: 2 residues within 4Å: Chain D: W.33, R.72 2 PLIP interactions: 2 interactions with chain D Water bridges: D:R.72 Salt bridges: D:R.72

4 x R3N: (2R,5S)-2-[(1S,2R)-1-carboxy-2-hydroxy-propyl]-5-[(2R)-tetrahydrofuran-2-yl]-2,5-dihydrothiazole-4-carboxylic acid(Non-covalent)

R3N.7: 16 residues within 4Å: Chain A: Y.13, V.15, W.19, H.86, H.88, D.90, H.91, F.126, I.130, H.162, S.187, S.189, P.191, H.227 Ligands: ZN.1, ZN.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.126, A:I.130 Hydrogen bonds: A:Y.13, A:S.187, A:S.189 Salt bridges: A:H.86, A:H.91, A:H.162, A:H.227 R3N.14: 16 residues within 4Å: Chain B: Y.13, V.15, W.19, H.86, H.88, D.90, H.91, F.126, I.130, H.162, S.187, S.189, P.191, H.227 Ligands: ZN.8, ZN.9 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.126, B:I.130 Hydrogen bonds: B:Y.13, B:S.187, B:S.189 Salt bridges: B:H.86, B:H.91, B:H.162, B:H.227 R3N.21: 16 residues within 4Å: Chain C: Y.13, V.15, W.19, H.86, H.88, D.90, H.91, F.126, I.130, H.162, S.187, S.189, P.191, H.227 Ligands: ZN.15, ZN.16 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.126, C:I.130 Hydrogen bonds: C:Y.13, C:S.187, C:S.189 Salt bridges: C:H.86, C:H.91, C:H.162, C:H.227 R3N.28: 16 residues within 4Å: Chain D: Y.13, V.15, W.19, H.86, H.88, D.90, H.91, F.126, I.130, H.162, S.187, S.189, P.191, H.227 Ligands: ZN.22, ZN.23 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:F.126, D:I.130 Hydrogen bonds: D:Y.13, D:S.187, D:S.189 Salt bridges: D:H.86, D:H.91, D:H.162, D:H.227

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lucic, A. et al., Faropenem reacts with serine and metallo-beta-lactamases to give multiple products. Eur.J.Med.Chem. (2021)

Release Date

2021-02-24

Peptides

Metallo-beta-lactamase L1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Metallo-beta-lactamase L1

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