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

Structure of NDM-1 in complex with macrocycle inhibitor NDM1i-3D

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x DCY- PRO- LWI- HYP- GLU- DPR- DLY- NLE: Macrocycle NDM1i-3D(Non-covalent)

DCY-PRO-LWI-HYP-GLU-DPR-DLY-NLE.1: 12 residues within 4Å: Chain A: M.45, P.46, F.48, V.51, W.71, H.100, D.102, G.197, N.198, H.228 Ligands: ZN.2, CD.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:M.45, A:P.46, A:V.51, A:W.71, A:N.198 Hydrogen bonds: A:N.198 Water bridges: A:N.198 Salt bridges: A:H.167, A:H.228

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 7 residues within 4Å: Chain A: H.98, H.100, D.102, H.167, C.186 Ligands: DCY-PRO-LWI-HYP-GLU-DPR-DLY-NLE.1, CD.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.98, A:H.100, A:H.167, H2O.7

1 x CD: CADMIUM ION(Non-covalent)

CD.3: 5 residues within 4Å: Chain A: D.102, C.186, H.228 Ligands: DCY-PRO-LWI-HYP-GLU-DPR-DLY-NLE.1, ZN.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.102, A:C.186, A:H.228, H2O.6, H2O.7

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
A

BlaNDM-4_1_JQ348841

Related Entries With Identical Sequence