SMTL ID : 6xbf.4 (3 other biounits)

Structure of NDM-1 in complex with macrocycle inhibitor NDM1i-1G

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x DAR- DAR- LEU- DCY- PRO- ILE- PRO- GLU: macrocycle inhibitor NDM1i-1G(Non-covalent)

DAR-DAR-LEU-DCY-PRO-ILE-PRO-GLU.1: 16 residues within 4Å: Chain A: L.43, M.45, F.48, V.51, W.71, H.100, Q.101, D.102, H.167, C.186, N.198, G.200, D.201, H.228 Ligands: ZN.2, ZN.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.43, A:M.45, A:F.48, A:V.51 Hydrogen bonds: A:N.198, A:G.200, A:D.201 Water bridges: A:Q.101 Salt bridges: A:D.201

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.98, H.100, H.167 Ligands: DAR-DAR-LEU-DCY-PRO-ILE-PRO-GLU.1, ZN.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.98, A:H.100, A:H.167 ZN.3: 5 residues within 4Å: Chain A: D.102, C.186, H.228 Ligands: DAR-DAR-LEU-DCY-PRO-ILE-PRO-GLU.1, ZN.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.102, A:C.186, A:H.228, H2O.2 ZN.4: 2 residues within 4Å: Chain A: E.130, D.201 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.130, A:E.130, A:D.201, A:D.201, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mulligan, V.K. et al., Computationally designed peptide macrocycle inhibitors of New Delhi metallo-beta-lactamase 1. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-03-31

Peptides

BlaNDM-4_1_JQ348841: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

BlaNDM-4_1_JQ348841

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