SMTL ID : 6eum.1

CRYSTAL STRUCTURE OF BCII METALLO-BETA-LACTAMASE IN COMPLEX WITH DZ-307

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.18 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.90, C.168, H.210 Ligands: ZN.2, BY5.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.90, A:H.210, BY5.4 ZN.2: 7 residues within 4Å: Chain A: H.86, H.88, D.90, H.149, C.168 Ligands: ZN.1, BY5.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.86, A:H.88, A:H.149

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

SO4.3: 2 residues within 4Å: Chain A: K.139, Q.160 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.160 Salt bridges: A:K.139

1 x BY5: (~{Z})-2-sulfanyl-3-[2,3,6-tris(fluoranyl)phenyl]prop-2-enoic acid(Covalent)

BY5.4: 12 residues within 4Å: Chain A: W.59, H.86, H.88, A.89, D.90, H.149, C.168, K.171, N.180, H.210 Ligands: ZN.1, ZN.2 6 PLIP interactions: 6 interactions with chain A Water bridges: A:N.180 Salt bridges: A:H.149, A:K.171, A:H.210 pi-Stacking: A:H.88 Halogen bonds: A:N.180

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: K.65, E.100, R.101 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.101, A:R.101 GOL.6: 7 residues within 4Å: Chain A: H.86, A.87, H.88, N.118, T.150, D.152, D.183 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.87, A:N.118, A:T.150, A:T.150 Water bridges: A:L.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, D. et al., Structure activity relationship studies on rhodanines and derived enethiol inhibitors of metallo-beta-lactamases. Bioorg. Med. Chem. (2018)

Release Date

2018-10-03

Peptides

Metallo-beta-lactamase type 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Metallo-beta-lactamase type 2

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