SMTL ID : 6uaf.1

Crystal Structure of the Metallo-beta-lactamase L1 from Stenotrophomonas maltophilia in the Complex with Hydrolyzed Imipnem

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

4 x HIW: (2R,4S)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-4-[(2-{[(Z)-iminomethyl]amino}ethyl)sulfanyl]-3,4-dihydro-2H-pyrrole-5-ca rboxylic acid(Non-covalent)

HIW.1: 14 residues within 4Å: Chain A: Y.35, W.41, H.108, D.112, H.113, F.148, I.152, H.184, S.209, S.211, P.213, H.249 Ligands: ZN.2, ZN.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.148, A:I.152, A:P.213 Hydrogen bonds: A:Y.35, A:Y.35, A:S.209, A:S.211 Salt bridges: A:H.108, A:H.113, A:H.184, A:H.249 HIW.4: 14 residues within 4Å: Chain B: Y.35, W.41, H.108, D.112, H.113, F.148, I.152, H.184, S.209, S.211, P.213, H.249 Ligands: ZN.5, ZN.6 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.148, B:I.152, B:P.213 Hydrogen bonds: B:Y.35, B:Y.35, B:S.209, B:S.211 Salt bridges: B:H.108, B:H.113, B:H.184, B:H.249 HIW.7: 14 residues within 4Å: Chain C: Y.35, W.41, H.108, D.112, H.113, F.148, I.152, H.184, S.209, S.211, P.213, H.249 Ligands: ZN.8, ZN.9 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:F.148, C:I.152, C:P.213 Hydrogen bonds: C:Y.35, C:S.209, C:S.211 Salt bridges: C:H.108, C:H.113, C:H.184, C:H.249 HIW.10: 14 residues within 4Å: Chain D: Y.35, W.41, H.108, D.112, H.113, F.148, I.152, H.184, S.209, S.211, P.213, H.249 Ligands: ZN.11, ZN.12 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:F.148, D:I.152, D:P.213 Hydrogen bonds: D:Y.35, D:S.209, D:S.211 Salt bridges: D:H.108, D:H.113, D:H.184, D:H.249

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: D.112, H.113, H.249 Ligands: HIW.1, ZN.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.112, A:H.113, A:H.249, H2O.1 ZN.3: 6 residues within 4Å: Chain A: H.108, H.110, H.113, H.184 Ligands: HIW.1, ZN.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.108, A:H.110, A:H.184, H2O.1 ZN.5: 5 residues within 4Å: Chain B: D.112, H.113, H.249 Ligands: HIW.4, ZN.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.112, B:H.113, B:H.249, H2O.9 ZN.6: 6 residues within 4Å: Chain B: H.108, H.110, H.113, H.184 Ligands: HIW.4, ZN.5 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.108, B:H.110, B:H.184, H2O.9 ZN.8: 5 residues within 4Å: Chain C: D.112, H.113, H.249 Ligands: HIW.7, ZN.9 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.112, C:H.113, C:H.249, H2O.18 ZN.9: 6 residues within 4Å: Chain C: H.108, H.110, H.113, H.184 Ligands: HIW.7, ZN.8 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.108, C:H.110, C:H.184, H2O.18 ZN.11: 5 residues within 4Å: Chain D: D.112, H.113, H.249 Ligands: HIW.10, ZN.12 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.112, D:H.113, D:H.249, H2O.26 ZN.12: 6 residues within 4Å: Chain D: H.108, H.110, H.113, H.184 Ligands: HIW.10, ZN.11 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.108, D:H.110, D:H.184, H2O.26

Links

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Citation

Kim, Y. et al., Crystal Structure of the Metallo-beta-lactamase L1 from Stenotrophomonas maltophilia in the Complex with Hydrolyzed Imipnem. To Be Published

Release Date

2019-09-18

Peptides

Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)