› 5nf0

X-ray diffraction
1.27Å 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/pdb5nf0/pdb
PDB entry 5nf0 coloured by chain, front view.
PDB entry 5nf0 coloured by chain, side view.
PDB entry 5nf0 coloured by chain, top view.
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 octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-166025 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Calcium-mediated lectin 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
CYD-TRP-TRD-LYS-LYD-LYS-LYD-LYS-TRD-TRP-CYD-GLY Chains: E, G, H
Molecule details ›
Chains: E, G, H
Length: 12 amino acids
Theoretical weight: 1.61 KDa
Source organism: synthetic construct
Expression system: Not provided
Fragment of ligand Chain: F
Molecule details ›
Chain: F
Length: 5 amino acids
Theoretical weight: 303 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand CA 8 x CA
Ligand ZDC 4 x ZDC
Ligand OXE 3 x OXE
3 modified residues:
Ligand DCY 6 x DCY
Ligand DTR 6 x DTR
Ligand DLY 6 x DLY

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P212121
Unit cell:
a: 45.278Å b: 99.966Å c: 106.611Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.164 0.163 0.184
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

5 review citations

The multifaceted nature of antimicrobial peptides: current synthetic chemistry approaches and future directions.
Gan et al. (2021)
4 more

2 mentions without citation

Bent Into Shape: Folded Peptides to Mimic Protein Structure and Modulate Protein Function.
Merritt et al. (2020)
1 more