SMTL ID : 7zo6.1

L1 metallo-beta-lactamase in complex with hydrolysed cefoxitin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.61 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, JNX.4 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, JNX.4 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: 7 residues within 4Å: Chain B: H.86, D.90, H.91, S.187, H.227 Ligands: ZN.6, JNX.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.7 ZN.6: 6 residues within 4Å: Chain B: H.86, H.88, H.91, H.162 Ligands: ZN.5, JNX.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.7 ZN.9: 7 residues within 4Å: Chain C: H.86, D.90, H.91, S.187, H.227 Ligands: ZN.10, JNX.12 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.90, C:H.91, C:H.227, H2O.14 ZN.10: 6 residues within 4Å: Chain C: H.86, H.88, H.91, H.162 Ligands: ZN.9, JNX.12 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.86, C:H.88, C:H.162, H2O.14 ZN.13: 7 residues within 4Å: Chain D: H.86, D.90, H.91, S.187, H.227 Ligands: ZN.14, JNX.16 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.90, D:H.91, D:H.227, H2O.21 ZN.14: 6 residues within 4Å: Chain D: H.86, H.88, H.91, H.162 Ligands: ZN.13, JNX.16 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.86, D:H.88, D:H.162, H2O.21

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

SO4.3: 4 residues within 4Å: Chain A: R.139, V.146, I.147, T.148 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.148, A:T.148 Water bridges: A:R.139, A:V.146 Salt bridges: A:R.139 SO4.7: 4 residues within 4Å: Chain B: R.139, V.146, I.147, T.148 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.148, B:T.148 Water bridges: B:R.139, B:V.146 Salt bridges: B:R.139 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:E.145, C:V.146 Salt bridges: C:R.139 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:E.145, D:V.146 Salt bridges: D:R.139

4 x JNX: (2~{R},5~{S})-5-(aminocarbonyloxymethyl)-2-[(1~{S})-1-methoxy-2-oxidanyl-2-oxidanylidene-1-(2-thiophen-2-ylethanoylamino)ethyl]-5,6-dihydro-2~{H}-1,3-thiazine-4-carboxylic acid(Non-covalent)

JNX.4: 18 residues within 4Å: Chain A: Y.13, V.15, W.19, H.86, H.88, A.89, D.90, H.91, F.126, I.130, H.162, S.187, S.189, P.191, G.192, H.227 Ligands: ZN.1, ZN.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.126, A:I.130 Hydrogen bonds: A:Y.13, A:S.187, A:S.189 Salt bridges: A:H.86, A:H.88, A:H.91, A:H.162, A:H.162, A:H.227 JNX.8: 18 residues within 4Å: Chain B: Y.13, V.15, W.19, H.86, H.88, A.89, D.90, H.91, F.126, I.130, H.162, S.187, S.189, P.191, G.192, H.227 Ligands: ZN.5, ZN.6 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.126, B:I.130 Hydrogen bonds: B:Y.13, B:S.187, B:S.189 Salt bridges: B:H.86, B:H.88, B:H.91, B:H.162, B:H.162, B:H.227 JNX.12: 18 residues within 4Å: Chain C: Y.13, V.15, W.19, H.86, H.88, A.89, D.90, H.91, F.126, I.130, H.162, S.187, S.189, P.191, G.192, H.227 Ligands: ZN.9, ZN.10 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:F.126, C:I.130 Hydrogen bonds: C:Y.13, C:S.187, C:S.189 Salt bridges: C:H.86, C:H.88, C:H.91, C:H.162, C:H.162, C:H.227 JNX.16: 18 residues within 4Å: Chain D: Y.13, V.15, W.19, H.86, H.88, A.89, D.90, H.91, F.126, I.130, H.162, S.187, S.189, P.191, G.192, H.227 Ligands: ZN.13, ZN.14 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:F.126, D:I.130 Hydrogen bonds: D:Y.13, D:S.187, D:S.189 Water bridges: D:H.86, D:H.91 Salt bridges: D:H.86, D:H.88, D:H.91, D:H.162, D:H.162, D:H.227

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hinchliffe, P. et al., Interactions of hydrolyzed beta-lactams with the L1 metallo-beta-lactamase: Crystallography supports stereoselective binding of cephem/carbapenem products. J.Biol.Chem. (2023)

Release Date

2023-03-08

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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