SMTL ID : 5hh5.1

Crystal structure of B3 metallo-beta-lactamase L1 complexed 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: 60M.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.8: 4 residues within 4Å: Chain B: H.86, H.88, H.162 Ligands: 60M.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.11 ZN.15: 4 residues within 4Å: Chain C: H.86, H.88, H.162 Ligands: 60M.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.22 ZN.22: 4 residues within 4Å: Chain D: H.86, H.88, H.162 Ligands: 60M.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.33

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

SO4.2: 4 residues within 4Å: Chain A: R.139, V.146, I.147, T.148 Ligand excluded by PLIP SO4.3: 2 residues within 4Å: Chain A: W.33, R.72 Ligand excluded by PLIP SO4.4: 6 residues within 4Å: Chain A: R.175, A.239, R.240, A.241, G.242, A.243 Ligand excluded by PLIP SO4.5: 1 residues within 4Å: Chain A: R.216 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain B: R.139, V.146, I.147, T.148 Ligand excluded by PLIP SO4.10: 2 residues within 4Å: Chain B: W.33, R.72 Ligand excluded by PLIP SO4.11: 6 residues within 4Å: Chain B: R.175, A.239, R.240, A.241, G.242, A.243 Ligand excluded by PLIP SO4.12: 1 residues within 4Å: Chain B: R.216 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain C: R.139, V.146, I.147, T.148 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain C: W.33, R.72 Ligand excluded by PLIP SO4.18: 6 residues within 4Å: Chain C: R.175, A.239, R.240, A.241, G.242, A.243 Ligand excluded by PLIP SO4.19: 1 residues within 4Å: Chain C: R.216 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain D: R.139, V.146, I.147, T.148 Ligand excluded by PLIP SO4.24: 2 residues within 4Å: Chain D: W.33, R.72 Ligand excluded by PLIP SO4.25: 6 residues within 4Å: Chain D: R.175, A.239, R.240, A.241, G.242, A.243 Ligand excluded by PLIP SO4.26: 1 residues within 4Å: Chain D: R.216 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: R.100 Chain C: A.137, D.138, R.139, I.140 Chain D: R.118, D.122 8 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: D:D.122, C:I.140, C:I.140 Water bridges: D:R.118, D:D.122, D:D.122, D:R.200, A:R.100 GOL.13: 7 residues within 4Å: Chain B: R.100 Chain C: R.118, D.122 Chain D: A.137, D.138, R.139, I.140 8 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B, 2 interactions with chain D Hydrogen bonds: C:D.122, D:I.140, D:I.140 Water bridges: C:R.118, C:D.122, C:D.122, C:R.200, B:R.100 GOL.20: 7 residues within 4Å: Chain A: A.137, D.138, R.139, I.140 Chain B: R.118, D.122 Chain C: R.100 7 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A, 1 interactions with chain C Water bridges: B:R.118, B:D.122, B:D.122, B:R.200, C:R.100 Hydrogen bonds: A:I.140, A:I.140 GOL.27: 7 residues within 4Å: Chain A: R.118, D.122 Chain B: A.137, D.138, R.139, I.140 Chain D: R.100 7 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D, 2 interactions with chain B Water bridges: A:R.118, A:D.122, A:D.122, A:R.200, D:R.100 Hydrogen bonds: B:I.140, B:I.140

4 x 60M: 6-(phosphonomethyl)pyridine-2-carboxylic acid(Non-covalent)

60M.7: 12 residues within 4Å: Chain A: W.19, H.86, H.88, D.90, H.91, H.162, S.187, S.189, P.191, H.227, A.230 Ligands: ZN.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.187, A:S.187, A:S.189, A:H.227 Water bridges: A:S.189 pi-Stacking: A:H.227 60M.14: 12 residues within 4Å: Chain B: W.19, H.86, H.88, D.90, H.91, H.162, S.187, S.189, P.191, H.227, A.230 Ligands: ZN.8 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.187, B:S.187, B:S.189, B:H.227 Water bridges: B:S.189 pi-Stacking: B:H.227 60M.21: 12 residues within 4Å: Chain C: W.19, H.86, H.88, D.90, H.91, H.162, S.187, S.189, P.191, H.227, A.230 Ligands: ZN.15 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.187, C:S.187, C:S.189, C:H.227 Water bridges: C:S.189 pi-Stacking: C:H.227 60M.28: 12 residues within 4Å: Chain D: W.19, H.86, H.88, D.90, H.91, H.162, S.187, S.189, P.191, H.227, A.230 Ligands: ZN.22 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.187, D:S.187, D:S.189, D:H.227 Water bridges: D:S.189 pi-Stacking: D:H.227

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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