SMTL ID : 7afz.1

L1 metallo-b-lactamase with compound EBL-1306

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: H.86, D.90, H.91, S.187, H.227 Ligands: ZN.2, RBW.3 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.2: 6 residues within 4Å: Chain A: H.86, H.88, H.91, H.162 Ligands: ZN.1, RBW.3 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.6: 7 residues within 4Å: Chain B: H.86, D.90, H.91, S.187, H.227 Ligands: ZN.7, RBW.8 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.7: 6 residues within 4Å: Chain B: H.86, H.88, H.91, H.162 Ligands: ZN.6, RBW.8 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.11: 7 residues within 4Å: Chain C: H.86, D.90, H.91, S.187, H.227 Ligands: ZN.12, RBW.13 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.90, C:H.91, C:H.227, H2O.20 ZN.12: 6 residues within 4Å: Chain C: H.86, H.88, H.91, H.162 Ligands: ZN.11, RBW.13 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.86, C:H.88, C:H.162, H2O.20 ZN.16: 7 residues within 4Å: Chain D: H.86, D.90, H.91, S.187, H.227 Ligands: ZN.17, RBW.18 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.90, D:H.91, D:H.227, H2O.29 ZN.17: 6 residues within 4Å: Chain D: H.86, H.88, H.91, H.162 Ligands: ZN.16, RBW.18 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.86, D:H.88, D:H.162, H2O.29

4 x RBW: 3-[3-chloranyl-4-(methylsulfonylmethyl)phenyl]-7-propan-2-yl-1~{H}-indole-2-carboxylic acid(Non-covalent)

RBW.3: 18 residues within 4Å: Chain A: Y.13, W.19, H.86, H.88, D.90, H.91, F.126, I.130, H.162, S.187, S.189, P.191, H.227, G.229, A.230, K.258 Ligands: ZN.1, ZN.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.126, A:I.130 Hydrogen bonds: A:S.187, A:S.189 Salt bridges: A:H.86, A:H.91, A:H.162, A:H.227 pi-Stacking: A:W.19, A:H.227 RBW.8: 18 residues within 4Å: Chain B: Y.13, W.19, H.86, H.88, D.90, H.91, F.126, I.130, H.162, S.187, S.189, P.191, H.227, G.229, A.230, K.258 Ligands: ZN.6, ZN.7 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.126, B:I.130 Hydrogen bonds: B:S.187, B:S.189 Salt bridges: B:H.86, B:H.91, B:H.162, B:H.227 pi-Stacking: B:W.19, B:H.227 RBW.13: 18 residues within 4Å: Chain C: Y.13, W.19, H.86, H.88, D.90, H.91, F.126, I.130, H.162, S.187, S.189, P.191, H.227, G.229, A.230, K.258 Ligands: ZN.11, ZN.12 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:F.126, C:I.130 Hydrogen bonds: C:S.187, C:S.189 Salt bridges: C:H.86, C:H.91, C:H.162, C:H.227 pi-Stacking: C:W.19, C:H.227 RBW.18: 18 residues within 4Å: Chain D: Y.13, W.19, H.86, H.88, D.90, H.91, F.126, I.130, H.162, S.187, S.189, P.191, H.227, G.229, A.230, K.258 Ligands: ZN.16, ZN.17 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:F.126, D:I.130 Hydrogen bonds: D:S.187, D:S.189 Salt bridges: D:H.86, D:H.91, D:H.162, D:H.227 pi-Stacking: D:W.19, D:H.227

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

SO4.4: 4 residues within 4Å: Chain A: R.139, V.146, I.147, T.148 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.239, A:G.242, A:A.243 Water bridges: A:A.241, A:A.241 SO4.9: 4 residues within 4Å: Chain B: R.139, V.146, I.147, T.148 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: 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 SO4.10: 5 residues within 4Å: Chain B: A.239, R.240, A.241, G.242, A.243 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.239, B:G.242, B:A.243 Water bridges: B:A.241, B:A.241 SO4.14: 4 residues within 4Å: Chain C: R.139, V.146, I.147, T.148 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: 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 SO4.15: 5 residues within 4Å: Chain C: A.239, R.240, A.241, G.242, A.243 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:A.239, C:G.242, C:A.243 Water bridges: C:A.241, C:A.241 SO4.19: 4 residues within 4Å: Chain D: R.139, V.146, I.147, T.148 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: 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 SO4.20: 5 residues within 4Å: Chain D: A.239, R.240, A.241, G.242, A.243 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:A.239, D:G.242, D:A.243 Water bridges: D:A.241, D:A.241

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brem, J. et al., Imitation of beta-lactam binding enables broad-spectrum metallo-beta-lactamase inhibitors. Nat.Chem. (2022)

Release Date

2021-10-06

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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