SMTL ID : 5hh6.1

Crystal structure of B3 metallo-beta-lactamase L1 in complex with a phosphonate-based inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.86, H.88, H.162 Ligands: 60N.2 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.5: 4 residues within 4Å: Chain B: H.86, H.88, H.162 Ligands: 60N.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.86, B:H.88, B:H.162, H2O.11 ZN.9: 4 residues within 4Å: Chain C: H.86, H.88, H.162 Ligands: 60N.10 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.86, C:H.88, C:H.162, H2O.21 ZN.13: 4 residues within 4Å: Chain D: H.86, H.88, H.162 Ligands: 60N.14 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.86, D:H.88, D:H.162, H2O.31

4 x 60N: 6-[(~{S})-oxidanyl(phosphono)methyl]pyridine-2-carboxylic acid(Non-covalent)

60N.2: 12 residues within 4Å: Chain A: H.86, H.88, D.90, H.91, H.162, S.187, L.188, S.189, P.191, H.227, A.230 Ligands: ZN.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.187, A:L.188, A:S.189 Water bridges: A:S.189 pi-Stacking: A:H.227 60N.6: 12 residues within 4Å: Chain B: H.86, H.88, D.90, H.91, H.162, S.187, L.188, S.189, P.191, H.227, A.230 Ligands: ZN.5 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.187, B:L.188, B:S.189 Water bridges: B:S.189 pi-Stacking: B:H.227 60N.10: 12 residues within 4Å: Chain C: H.86, H.88, D.90, H.91, H.162, S.187, L.188, S.189, P.191, H.227, A.230 Ligands: ZN.9 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.187, C:L.188, C:S.189 Water bridges: C:Y.13, C:S.189 pi-Stacking: C:H.227 60N.14: 12 residues within 4Å: Chain D: H.86, H.88, D.90, H.91, H.162, S.187, L.188, S.189, P.191, H.227, A.230 Ligands: ZN.13 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.187, D:L.188, D:S.189 Water bridges: D:Y.13, D:S.189 pi-Stacking: D:H.227

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

SO4.3: 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 SO4.4: 2 residues within 4Å: Chain A: W.33, R.72 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.72, A:R.72 Salt bridges: A:R.72 SO4.7: 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 SO4.8: 2 residues within 4Å: Chain B: W.33, R.72 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.72, B:R.72 Salt bridges: B:R.72 SO4.11: 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 SO4.12: 2 residues within 4Å: Chain C: W.33, R.72 3 PLIP interactions: 3 interactions with chain C Water bridges: C:R.72, C:R.72 Salt bridges: C:R.72 SO4.15: 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 SO4.16: 2 residues within 4Å: Chain D: W.33, R.72 3 PLIP interactions: 3 interactions with chain D Water bridges: D:R.72, D:R.72 Salt bridges: D:R.72

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hinchliffe, P. et al., Structural and Kinetic Studies of the Potent Inhibition of Metallo-beta-lactamases by 6-Phosphonomethylpyridine-2-carboxylates. Biochemistry (2018)

Release Date

2017-01-18

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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