SMTL ID : 5b15.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.39 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, DQM.13 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, DQM.13 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.76, A:H.77, A:H.215, H2O.1

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

NA.3: 5 residues within 4Å: Chain A: S.82, Q.85, K.86, S.123, A.124 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.82, A:A.124 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: 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.6: 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:V.179, A:V.179 Water bridges: A:Q.113 NA.7: 2 residues within 4Å: Chain A: N.219, A.244 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.219, A:R.224 NA.8: 6 residues within 4Å: Chain A: R.103, A.124, K.125, V.126, R.127 Ligands: SO4.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.103, A:K.125, A:V.126, A:R.127 NA.9: 5 residues within 4Å: Chain A: S.73, A.97, N.98, T.101, P.108 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.73, A:A.97 Water bridges: A:T.101, A:E.152

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

SO4.10: 2 residues within 4Å: Chain A: T.177, R.252 3 PLIP interactions: 3 interactions with chain A Water bridges: A:A.248, A:A.248 Salt bridges: A:R.252 SO4.11: 4 residues within 4Å: Chain A: A.124, K.125, R.127 Ligands: NA.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.125 Salt bridges: A:R.127 SO4.12: 4 residues within 4Å: Chain A: R.56, K.61, L.62, S.63 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.62, A:S.63 Water bridges: A:R.56

1 x DQM: (2~{S},3~{R},4~{S})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-3-methyl-4-[(3~{S},5~{S})-5-[(sulfamoylamino)methyl]pyrrolidin-3-yl]sulfanyl-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid(Non-covalent)

DQM.13: 14 residues within 4Å: Chain A: W.5, H.72, H.74, D.76, H.77, Q.113, H.150, S.175, T.177, H.215, E.217, R.252 Ligands: ZN.1, ZN.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.5 Hydrogen bonds: A:Q.113, A:S.175, A:E.217, A:E.217 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 Doripenem. 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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