SMTL ID : 7o0o.1

Crystal structure of the B3 metallo-beta-lactamase L1 with hydrolysed ertapenem

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 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, 9XS.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.86, A:H.88, A:H.162 ZN.2: 6 residues within 4Å: Chain A: H.86, D.90, H.91, H.227 Ligands: ZN.1, 9XS.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.90, A:H.91, A:H.227 ZN.3: 2 residues within 4Å: Chain A: D.30, H.31 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.31, H2O.11 ZN.7: 6 residues within 4Å: Chain B: H.86, H.88, H.91, H.162 Ligands: ZN.8, 9XS.10 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.86, B:H.88, B:H.162 ZN.8: 6 residues within 4Å: Chain B: H.86, D.90, H.91, H.227 Ligands: ZN.7, 9XS.10 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.90, B:H.91, B:H.227 ZN.9: 2 residues within 4Å: Chain B: D.30, H.31 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.31, H2O.22 ZN.13: 6 residues within 4Å: Chain C: H.86, H.88, H.91, H.162 Ligands: ZN.14, 9XS.16 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.86, C:H.88, C:H.162 ZN.14: 6 residues within 4Å: Chain C: H.86, D.90, H.91, H.227 Ligands: ZN.13, 9XS.16 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.90, C:H.91, C:H.227 ZN.15: 2 residues within 4Å: Chain C: D.30, H.31 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.31, H2O.33 ZN.19: 6 residues within 4Å: Chain D: H.86, H.88, H.91, H.162 Ligands: ZN.20, 9XS.22 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.86, D:H.88, D:H.162 ZN.20: 6 residues within 4Å: Chain D: H.86, D.90, H.91, H.227 Ligands: ZN.19, 9XS.22 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.90, D:H.91, D:H.227 ZN.21: 2 residues within 4Å: Chain D: D.30, H.31 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.31, H2O.44

4 x 9XS: (2~{S},3~{R},4~{S})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-[(3~{S},5~{S})-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl]sulfanyl-3-methyl-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid(Non-covalent)

9XS.4: 16 residues within 4Å: Chain A: Y.13, W.19, H.86, H.88, A.89, D.90, H.91, F.126, I.130, H.162, S.187, S.189, P.191, H.227 Ligands: ZN.1, ZN.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.126, A:I.130, A:P.191 Hydrogen bonds: A:Y.13, A:S.187, A:S.189, A:S.189 Salt bridges: A:H.86, A:H.86, A:H.88, A:H.91, A:H.162, A:H.162, A:H.227 9XS.10: 16 residues within 4Å: Chain B: Y.13, W.19, H.86, H.88, A.89, D.90, H.91, F.126, I.130, H.162, S.187, S.189, P.191, H.227 Ligands: ZN.7, ZN.8 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.126, B:I.130, B:P.191 Hydrogen bonds: B:Y.13, B:S.187, B:S.189, B:S.189 Salt bridges: B:H.86, B:H.86, B:H.88, B:H.91, B:H.162, B:H.162, B:H.227 9XS.16: 16 residues within 4Å: Chain C: Y.13, W.19, H.86, H.88, A.89, D.90, H.91, F.126, I.130, H.162, S.187, S.189, P.191, H.227 Ligands: ZN.13, ZN.14 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:F.126, C:I.130, C:P.191 Hydrogen bonds: C:Y.13, C:S.187, C:S.189, C:S.189 Salt bridges: C:H.86, C:H.86, C:H.88, C:H.91, C:H.162, C:H.162, C:H.227 9XS.22: 16 residues within 4Å: Chain D: Y.13, W.19, H.86, H.88, A.89, D.90, H.91, F.126, I.130, H.162, S.187, S.189, P.191, H.227 Ligands: ZN.19, ZN.20 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:F.126, D:I.130, D:P.191 Hydrogen bonds: D:Y.13, D:S.187, D:S.189, D:S.189 Salt bridges: D:H.86, D:H.86, D:H.88, D:H.91, D:H.162, D:H.162, D:H.227

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

SO4.5: 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 SO4.6: 6 residues within 4Å: Chain A: R.175, A.239, R.240, A.241, G.242, A.243 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:A.239, A:G.242 Water bridges: A:R.175, A:R.175, A:A.241, A:A.241 Salt bridges: A:R.175 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: 6 residues within 4Å: Chain B: R.175, A.239, R.240, A.241, G.242, A.243 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:A.239, B:G.242 Water bridges: B:R.175, B:R.175, B:A.241, B:A.241 Salt bridges: B:R.175 SO4.17: 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 SO4.18: 6 residues within 4Å: Chain C: R.175, A.239, R.240, A.241, G.242, A.243 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:A.239, C:G.242 Water bridges: C:R.175, C:R.175, C:A.241, C:A.241 Salt bridges: C:R.175 SO4.23: 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 SO4.24: 6 residues within 4Å: Chain D: R.175, A.239, R.240, A.241, G.242, A.243 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:A.239, D:G.242 Water bridges: D:R.175, D:R.175, D:A.241, D:A.241 Salt bridges: D:R.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Twidale, R.M. et al., Crystallography and QM/MM Simulations Identify Preferential Binding of Hydrolyzed Carbapenem and Penem Antibiotics to the L1 Metallo-beta-Lactamase in the Imine Form. J.Chem.Inf.Model. (2021)

Release Date

2021-10-13

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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