› 5ney

X-ray diffraction
1.55Å resolution

Discovery, crystal structures and atomic force microscopy study of thioether ligated D,L-cyclic antimicrobial peptides against multidrug resistant Pseudomonas aeruginosa

Released:
DOI: 10.2210/pdb5ney/pdb
PDB 5ney coloured by chain and viewed from the front.
PDB 5ney coloured by chain and viewed from the side.
PDB 5ney coloured by chain and viewed from the top.
Source organisms:
Primary publication:
Design, crystal structure and atomic force microscopy study of thioether ligated d,l-cyclic antimicrobial peptides against multidrug resistant Pseudomonas aeruginosa.
He R, Di Bonaventura I, Visini R, Gan BH, Fu Y, Probst D, Lüscher A, Köhler T, van Delden C, Stocker A, Hong W, Darbre T, Reymond JL
Chem Sci 8 7464-7475 (2017)
PMID: 29163899

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
PA-IIL domain-containing protein Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 114 amino acids
Theoretical weight: 11.73 KDa
Source organism: Pseudomonas aeruginosa
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9HYN5 (Residues: 2-115; Coverage: 99%)
Gene names: PA3361, lecB
Sequence domains: Fucose-binding lectin II (PA-IIL)
Structure domains: Calcium-mediated lectin
CYS-TRD-TRP-LYD-LYS-LYD-LYS-LYD-TRP-TRD-CYS-ALA Chain: E
Molecule details ›
Chain: E
Length: 12 amino acids
Theoretical weight: 1.68 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand ZDC 4 x ZDC
Ligand CA 8 x CA
Ligand OXE 1 x OXE
2 modified residues:
Ligand DTR 2 x DTR
Ligand DLY 3 x DLY

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: C2
Unit cell:
a: 94.925Å b: 45.748Å c: 103.85Å
α: 90° β: 114.98° γ: 90°
R-values:
R R work R free
0.186 0.185 0.217
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Engineered Cationic Antimicrobial Peptides (eCAPs) to Combat Multidrug-Resistant Bacteria.
Deslouches et al. (2020)
1 more