SMTL ID : 8ofe.1

E.coli Peptide Deformylase with bound inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x VLK: (2R)-2-[[methanoyl(oxidanyl)amino]methyl]-N-[(2S)-3-methyl-1-oxidanylidene-1-[2-(sulfanylmethyl)pyrrolidin-1-yl]butan-2-yl]heptanamide(Non-covalent)

VLK.1: 20 residues within 4Å: Chain A: E.44, E.45, G.46, I.47, G.48, L.49, Q.53, I.89, E.91, G.92, C.93, L.94, S.95, L.128, I.131, C.132, H.135, E.136, H.139 Ligands: ZN.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.94, A:I.131 Hydrogen bonds: A:I.47, A:Q.53, A:G.92, A:G.92, A:L.94

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: Q.53, C.93, L.94, H.135, H.139 Ligands: VLK.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.93, A:H.135, A:H.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kirschner, H. et al., Structural Insights into Antibacterial Payload Release from Gold Nanoparticles Bound to E. coli Peptide Deformylase. Chemmedchem (2024)

Release Date

2023-12-27

Peptides

Peptide deformylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Peptide deformylase

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