SMTL ID : 2hb9.1

Crystal Structure of the Zinc-Beta-Lactamase L1 from Stenotrophomonas Maltophilia (Inhibitor 3)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.84, H.86, H.160 Ligands: L13.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.84, A:H.86, A:H.160 ZN.2: 4 residues within 4Å: Chain A: D.88, H.89, H.225 Ligands: L13.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.88, A:H.89, A:H.225 ZN.7: 4 residues within 4Å: Chain B: H.84, H.86, H.160 Ligands: L13.11 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.84, B:H.86, B:H.160 ZN.8: 4 residues within 4Å: Chain B: D.88, H.89, H.225 Ligands: L13.11 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.88, B:H.89, B:H.225 ZN.13: 4 residues within 4Å: Chain C: H.84, H.86, H.160 Ligands: L13.17 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.84, C:H.86, C:H.160 ZN.14: 4 residues within 4Å: Chain C: D.88, H.89, H.225 Ligands: L13.17 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.88, C:H.89, C:H.225 ZN.19: 4 residues within 4Å: Chain D: H.84, H.86, H.160 Ligands: L13.23 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.84, D:H.86, D:H.160 ZN.20: 4 residues within 4Å: Chain D: D.88, H.89, H.225 Ligands: L13.23 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.88, D:H.89, D:H.225

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

SO4.3: 4 residues within 4Å: Chain A: R.137, V.144, I.145, T.146 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.144, A:T.146, A:T.146 Water bridges: A:R.137, A:R.137 Salt bridges: A:R.137 SO4.4: 2 residues within 4Å: Chain A: W.31, R.70 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.70, A:R.70 Salt bridges: A:R.70 SO4.9: 4 residues within 4Å: Chain B: R.137, V.144, I.145, T.146 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:V.144, B:T.146, B:T.146 Water bridges: B:R.137, B:R.137 Salt bridges: B:R.137 SO4.10: 2 residues within 4Å: Chain B: W.31, R.70 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.70, B:R.70 Salt bridges: B:R.70 SO4.15: 4 residues within 4Å: Chain C: R.137, V.144, I.145, T.146 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:V.144, C:T.146 Water bridges: C:R.137, C:R.137 Salt bridges: C:R.137 SO4.16: 2 residues within 4Å: Chain C: W.31, R.70 3 PLIP interactions: 3 interactions with chain C Water bridges: C:R.70, C:R.70 Salt bridges: C:R.70 SO4.21: 4 residues within 4Å: Chain D: R.137, V.144, I.145, T.146 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:V.144, D:T.146 Water bridges: D:R.137, D:R.137 Salt bridges: D:R.137 SO4.22: 2 residues within 4Å: Chain D: W.31, R.70 3 PLIP interactions: 3 interactions with chain D Water bridges: D:R.70, D:R.70 Salt bridges: D:R.70

8 x L13: 4-AMINO-5-(2-METHYLPHENYL)-2,4-DIHYDRO-3H-1,2,4-TRIAZOLE-3-THIONE(Non-covalent)

L13.5: 12 residues within 4Å: Chain A: Y.11, W.17, H.84, H.86, D.88, H.89, F.124, I.128, H.160, H.225 Ligands: ZN.1, ZN.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.11, A:Y.11, A:F.124, A:I.128, A:I.128 L13.6: 11 residues within 4Å: Chain A: P.74, R.75, K.97, R.98, R.99, T.100, G.101 Chain D: R.78, K.103, D.136, R.137 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:K.103, D:K.103, D:D.136, D:R.137 Hydrogen bonds: D:R.78, D:R.78, A:R.98 L13.11: 12 residues within 4Å: Chain B: Y.11, W.17, H.84, H.86, D.88, H.89, F.124, I.128, H.160, H.225 Ligands: ZN.7, ZN.8 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.11, B:Y.11, B:F.124, B:I.128, B:I.128 L13.12: 11 residues within 4Å: Chain B: P.74, R.75, K.97, R.98, R.99, T.100, G.101 Chain C: R.78, K.103, D.136, R.137 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:K.103, C:K.103, C:D.136, C:R.137 Hydrogen bonds: C:R.78, C:R.78, B:R.98 L13.17: 12 residues within 4Å: Chain C: Y.11, W.17, H.84, H.86, D.88, H.89, F.124, I.128, H.160, H.225 Ligands: ZN.13, ZN.14 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:Y.11, C:Y.11, C:F.124, C:I.128, C:I.128 Hydrogen bonds: C:H.160, C:H.225 L13.18: 11 residues within 4Å: Chain B: R.78, K.103, D.136, R.137 Chain C: P.74, R.75, K.97, R.98, R.99, T.100, G.101 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:K.103, B:K.103, B:D.136, B:R.137 Hydrogen bonds: B:R.78, B:R.78, C:R.98 L13.23: 12 residues within 4Å: Chain D: Y.11, W.17, H.84, H.86, D.88, H.89, F.124, I.128, H.160, H.225 Ligands: ZN.19, ZN.20 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:Y.11, D:Y.11, D:F.124, D:I.128, D:I.128 L13.24: 11 residues within 4Å: Chain A: R.78, K.103, D.136, R.137 Chain D: P.74, R.75, K.97, R.98, R.99, T.100, G.101 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:K.103, A:K.103, A:D.136, A:R.137 Hydrogen bonds: A:R.78, A:R.78, D:R.98

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nauton, L. et al., Structural insights into the design of inhibitors for the L1 metallo-beta-lactamase from Stenotrophomonas maltophilia. J.Mol.Biol. (2008)

Release Date

2007-05-29

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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