SMTL ID : 5b1u.1

Crystal Structure of Metallo-beta-Lactamase SMB-1 Bound to Hydrolyzed Imipenem

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.72, H.74, H.77, H.150 Ligands: ZN.2, HIW.21 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.72, A:H.74, A:H.150, H2O.3 ZN.2: 5 residues within 4Å: Chain A: D.76, H.77, H.215 Ligands: ZN.1, HIW.21 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.76, A:H.77, A:H.215, H2O.3

15 x NA: SODIUM ION(Non-functional Binders)

NA.3: 6 residues within 4Å: Chain A: S.73, A.97, N.98, T.101, P.108 Ligands: NA.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.73, A:S.73 Water bridges: A:T.101, A:E.152 NA.4: 6 residues within 4Å: Chain A: S.70, T.71, A.94, G.95, G.153, I.155 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.71, A:G.95, A:I.155 Water bridges: A:N.98 NA.5: 5 residues within 4Å: Chain A: S.82, Q.85, K.86, S.123, A.124 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.82, A:K.86, A:A.124 NA.6: 6 residues within 4Å: Chain A: R.103, A.124, K.125, V.126, R.127 Ligands: SO4.19 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.103, A:R.103, A:K.125, A:V.126, A:R.127 NA.7: 4 residues within 4Å: Chain A: P.8, Q.9, V.50, N.54 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.9, A:N.54, A:N.54 NA.8: 5 residues within 4Å: Chain A: S.175, T.177, H.215, V.218 Ligands: HIW.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.175 Water bridges: A:L.176 NA.9: 4 residues within 4Å: Chain A: G.89, A.90, T.91, K.125 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.125 NA.10: 5 residues within 4Å: Chain A: S.183, Y.184, R.185, H.189 Ligands: NA.17 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.185, A:H.189 NA.11: 8 residues within 4Å: Chain A: S.73, H.74, T.101, S.107, P.108, D.111, T.151 Ligands: NA.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.111, A:D.111 NA.12: 4 residues within 4Å: Chain A: P.112, H.150, T.177, V.179 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.150, A:V.179 Water bridges: A:Q.113 NA.13: 5 residues within 4Å: Chain A: R.227, S.234, A.235, V.237 Ligands: NA.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.227, A:R.227, A:A.235 NA.14: 4 residues within 4Å: Chain A: D.220, M.221, W.222, T.223 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.222, A:T.223, A:T.223 NA.15: 3 residues within 4Å: Chain A: S.234, V.237 Ligands: NA.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.234 NA.16: 4 residues within 4Å: Chain A: E.231, G.232, N.233, S.234 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.231, A:N.233, A:S.234 NA.17: 3 residues within 4Å: Chain A: S.183, Y.184 Ligands: NA.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.183

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

SO4.18: 3 residues within 4Å: Chain A: T.177, R.252 Ligands: HIW.21 3 PLIP interactions: 3 interactions with chain A Water bridges: A:A.248, A:A.248 Salt bridges: A:R.252 SO4.19: 4 residues within 4Å: Chain A: A.124, K.125, R.127 Ligands: NA.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.125 Salt bridges: A:R.127 SO4.20: 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 Salt bridges: A:R.56, A:K.61

1 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.21: 18 residues within 4Å: Chain A: W.5, H.72, H.74, D.76, H.77, Q.113, L.117, H.150, S.175, T.177, H.215, E.217, V.218, R.252 Ligands: ZN.1, ZN.2, NA.8, SO4.18 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.117 Hydrogen bonds: A:H.74, A:Q.113, A:S.175 Water bridges: A:H.72, A:H.77 Salt bridges: A:H.72, A:H.77, A:H.150, A:H.215

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wachino, J. et al., Crystal Structure of Metallo-beta-Lactamase SMB-1 Bound to Hydrolyzed Imipenem. To be published

Release Date

2016-05-11

Peptides

Metallo-beta-lactamase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Metallo-beta-lactamase

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