› 6q6x

X-ray diffraction
1.52Å resolution

Structure of Fucosylated D-antimicrobial peptide SB6 in complex with the Fucose-binding lectin PA-IIL at 1.525 Angstrom resolution

Released:
DOI: 10.2210/pdb6q6x/pdb
PDB entry 6q6x coloured by chain, front view.
PDB entry 6q6x coloured by chain, side view.
PDB entry 6q6x coloured by chain, top view.
Source organisms:
Primary publication:
X-ray Crystal Structures of Short Antimicrobial Peptides as Pseudomonas aeruginosa Lectin B Complexes.
Baeriswyl S, Gan BH, Siriwardena TN, Visini R, Robadey M, Javor S, Stocker A, Darbre T, Reymond JL
ACS Chem Biol 14 758-766 (2019)
PMID: 30830745

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-167303 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
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 'BL21-Gold(DE3)pLysS AG'
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
SB6 Chains: E, F, G, H
Molecule details ›
Chains: E, F, G, H
Length: 12 amino acids
Theoretical weight: 1.43 KDa
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 NH2 4 x NH2
4 modified residues:
Ligand DLY 24 x DLY
Ligand DTY 4 x DTY
Ligand DAL 8 x DAL
Ligand DLE 12 x DLE

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P21
Unit cell:
a: 52.474Å b: 59.416Å c: 72.06Å
α: 90° β: 106.12° γ: 90°
R-values:
R R work R free
0.159 0.158 0.182
Expression systems:
  • Escherichia coli 'BL21-Gold(DE3)pLysS AG'
  • Not provided

Quick links

Citations

4 review citations

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