SMTL ID : 6ibs.2 (1 other biounit)

Crystal structure of NDM-1 beta-lactamase in complex with boronic inhibitor cpd 6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.37 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.98, C.182, H.224 Ligands: HB8.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.98, A:C.182, A:H.224 ZN.2: 4 residues within 4Å: Chain A: H.94, H.96, H.163 Ligands: HB8.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.94, A:H.96, A:H.163

1 x HB8: [7-[(2-methylpropan-2-yl)oxycarbonylamino]-1-benzothiophen-2-yl]-tris(oxidanyl)boranuide(Non-covalent)

HB8.3: 14 residues within 4Å: Chain A: L.39, M.41, V.47, W.67, H.94, H.96, Q.97, D.98, H.163, C.182, N.194, H.224 Ligands: ZN.1, ZN.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.39, A:Q.97 Water bridges: A:N.194 pi-Stacking: A:W.67

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 2 residues within 4Å: Chain A: E.126, D.197 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.126, A:E.126, A:D.197, A:D.197, H2O.6 CA.5: 2 residues within 4Å: Chain A: D.69, D.104 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.69, A:D.104, H2O.2, H2O.4, H2O.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cendron, L. et al., X-ray Crystallography Deciphers the Activity of Broad-Spectrum Boronic Acid beta-Lactamase Inhibitors. Acs Med.Chem.Lett. (2019)

Release Date

2019-04-24

Peptides

Metallo-beta-lactamase type 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Metallo-beta-lactamase type 2

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