SMTL ID : 5evb.1

Crystal structure of the metallo-beta-lactamase L1 in complex with the bisthiazolidine inhibitor D-CS319

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.86, H.88, H.162 Ligands: ZN.2, 3R9.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.86, A:H.88, A:H.162 ZN.2: 5 residues within 4Å: Chain A: D.90, H.91, H.227 Ligands: ZN.1, 3R9.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.90, A:H.91, A:H.227, H2O.5 ZN.6: 5 residues within 4Å: Chain B: H.86, H.88, H.162 Ligands: ZN.7, 3R9.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.86, B:H.88, B:H.162 ZN.7: 5 residues within 4Å: Chain B: D.90, H.91, H.227 Ligands: ZN.6, 3R9.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.90, B:H.91, B:H.227, H2O.17 ZN.11: 5 residues within 4Å: Chain C: H.86, H.88, H.162 Ligands: ZN.12, 3R9.13 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.86, C:H.88, C:H.162 ZN.12: 5 residues within 4Å: Chain C: D.90, H.91, H.227 Ligands: ZN.11, 3R9.13 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.90, C:H.91, C:H.227, H2O.30 ZN.16: 5 residues within 4Å: Chain D: H.86, H.88, H.162 Ligands: ZN.17, 3R9.18 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.86, D:H.88, D:H.162 ZN.17: 5 residues within 4Å: Chain D: D.90, H.91, H.227 Ligands: ZN.16, 3R9.18 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.90, D:H.91, D:H.227, H2O.42

4 x 3R9: (3S,5S,7aR)-5-(sulfanylmethyl)tetrahydro[1,3]thiazolo[4,3-b][1,3]thiazole-3-carboxylic acid(Non-covalent)

3R9.3: 12 residues within 4Å: Chain A: Y.13, H.86, H.88, D.90, H.91, F.126, I.130, H.162, P.191, H.227 Ligands: ZN.1, ZN.2 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.90 3R9.8: 12 residues within 4Å: Chain B: Y.13, H.86, H.88, D.90, H.91, F.126, I.130, H.162, P.191, H.227 Ligands: ZN.6, ZN.7 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:D.90 3R9.13: 12 residues within 4Å: Chain C: Y.13, H.86, H.88, D.90, H.91, F.126, I.130, H.162, P.191, H.227 Ligands: ZN.11, ZN.12 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.13 Salt bridges: C:D.90 3R9.18: 12 residues within 4Å: Chain D: Y.13, H.86, H.88, D.90, H.91, F.126, I.130, H.162, P.191, H.227 Ligands: ZN.16, ZN.17 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.13 Salt bridges: D:D.90

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

SO4.4: 4 residues within 4Å: Chain A: R.139, V.146, I.147, T.148 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.148, A:T.148, A:T.148 Water bridges: A:R.139, A:R.139 Salt bridges: A:R.139 SO4.5: 1 residues within 4Å: Chain A: G.177 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.176, A:G.177 SO4.9: 4 residues within 4Å: Chain B: R.139, V.146, I.147, T.148 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.148, B:T.148, B:T.148 Water bridges: B:R.139, B:R.139 Salt bridges: B:R.139 SO4.10: 1 residues within 4Å: Chain B: G.177 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.176, B:G.177 SO4.14: 4 residues within 4Å: Chain C: R.139, V.146, I.147, T.148 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.148, C:T.148 Water bridges: C:R.139, C:R.139 Salt bridges: C:R.139 SO4.15: 1 residues within 4Å: Chain C: G.177 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.176, C:G.177 SO4.19: 4 residues within 4Å: Chain D: R.139, V.146, I.147, T.148 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.148, D:T.148 Water bridges: D:R.139, D:R.139 Salt bridges: D:R.139 SO4.20: 1 residues within 4Å: Chain D: G.177 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.176, D:G.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hinchliffe, P. et al., Cross-class metallo-beta-lactamase inhibition by bisthiazolidines reveals multiple binding modes. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-06-01

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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