SMTL ID : 3vpe.1

Crystal Structure of Metallo-beta-Lactamase SMB-1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.72, H.74, Q.113, H.150 Ligands: ZN.2, GOL.9 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.72, A:H.74, A:H.150, H2O.1 ZN.2: 5 residues within 4Å: Chain A: D.76, H.77, H.215 Ligands: ZN.1, GOL.9 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.76, A:H.77, A:H.215, H2O.1, H2O.1

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

SO4.3: 4 residues within 4Å: Chain A: H.189, P.190, E.191, V.192 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.191, A:V.192 Water bridges: A:H.189 Salt bridges: A:H.189 SO4.4: 4 residues within 4Å: Chain A: R.56, K.61, L.62, S.63 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.62, A:S.63 Water bridges: A:S.63, A:S.63 Salt bridges: A:R.56 SO4.5: 5 residues within 4Å: Chain A: D.4, W.5, S.6, T.44, K.46 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.6, A:S.6, A:S.6 Water bridges: A:D.4, A:W.5 Salt bridges: A:K.46

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 6 residues within 4Å: Chain A: V.218, N.219, D.220, R.224, D.238, A.244 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.244 Hydrogen bonds: A:D.238 Water bridges: A:D.220 Salt bridges: A:R.224 ACT.7: 4 residues within 4Å: Chain A: A.178, V.179, S.180, R.256 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.179 Hydrogen bonds: A:S.180 Water bridges: A:A.178 Salt bridges: A:R.256 ACT.8: 6 residues within 4Å: Chain A: S.175, L.176, T.177, V.218, I.245, G.249 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.177, A:I.245 Hydrogen bonds: A:D.174, A:L.176

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 8 residues within 4Å: Chain A: W.5, Q.113, L.117, H.150, V.179, H.215 Ligands: ZN.1, ZN.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.113 Water bridges: A:Q.113, A:S.116, A:T.177, A:T.177 GOL.10: 3 residues within 4Å: Chain A: P.108, K.109, S.110 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.109, A:K.109, A:S.110, A:S.110 Water bridges: A:S.107, A:K.109 GOL.11: 2 residues within 4Å: Chain A: A.124, K.125 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.125 Water bridges: A:R.103, A:V.126 GOL.12: 5 residues within 4Å: Chain A: S.183, Y.184, R.185, D.188, H.189 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.185, A:R.185 Water bridges: A:H.189, A:H.189

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wachino, J. et al., Structural Insights into the Subclass B3 Metallo-beta-Lactamase SMB-1 and the Mode of Inhibition by the Common Metallo- -Lactamase Inhibitor Mercaptoacetate. Antimicrob.Agents Chemother. (2013)

Release Date

2013-02-13

Peptides

Metallo-beta-lactamase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Metallo-beta-lactamase

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