8AN9

Fucosylated mixed-chirality linear peptide FHP5 bound to the fucose binding lectin LecB PA-IIL from Pseudomonas aeruginosa at 1.3 Angstrom resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

To Fold or Not to Fold: Diastereomeric Optimization of an alpha-Helical Antimicrobial Peptide.

Personne, H.Paschoud, T.Fulgencio, S.Baeriswyl, S.Kohler, T.van Delden, C.Stocker, A.Javor, S.Reymond, J.L.

(2023) J Med Chem 66: 7570-7583

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c00460
  • Primary Citation of Related Structures:  
    8AN9, 8ANO, 8ANR, 8AOO

  • PubMed Abstract: 

    Membrane disruptive α-helical antimicrobial peptides (AMPs) offer an opportunity to address multidrug resistance; however, most AMPs are toxic and unstable in serum. These limitations can be partly overcome by introducing D-residues, which often confers protease resistance and reduces toxicity without affecting antibacterial activity, presumably due to lowered α-helicity. Here, we investigated 31 diastereomers of the α-helical AMP KKLLKLLKLLL. Three diastereomers containing two, three, and four D-residues showed increased antibacterial effects, comparable hemolysis, reduced toxicity against HEK293 cells, and excellent serum stability, while another diastereomer with four D-residues additionally displayed lower hemolysis. X-ray crystallography confirmed that high or low α-helicity as measured by circular dichroism indicated α-helical or disordered structures independently of the number of chirality switched residues. In contrast to previous reports, α-helicity across diastereomers correlated with both antibacterial activity and hemolysis and revealed a complex relationship between stereochemistry, activity, and toxicity, highlighting the potential of diastereomers for property optimization.


  • Organizational Affiliation

    Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fucose-binding lectin PA-IIL
A, B, C, D
114Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: lecBPA3361
UniProt
Find proteins for Q9HYN5 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HYN5 
Go to UniProtKB:  Q9HYN5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HYN5
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Mixed-chirality peptide FHP5
E, F, G
12synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZDC (Subject of Investigation/LOI)
Query on ZDC

Download Ideal Coordinates CCD File 
N [auth C],
Q [auth E],
R [auth F],
S [auth G]
3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid
C8 H14 O6
YTZUDUWVQZSKNN-OASCRQMUSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth B]
K [auth B]
L [auth C]
H [auth A],
I [auth A],
J [auth B],
K [auth B],
L [auth C],
M [auth C],
O [auth D],
P [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.766α = 90
b = 62.783β = 92.82
c = 64.226γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union885076
Swiss National Science FoundationSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-31
    Type: Initial release
  • Version 1.1: 2023-06-07
    Changes: Database references
  • Version 1.2: 2023-06-21
    Changes: Database references
  • Version 1.3: 2024-02-07
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-10-23
    Changes: Structure summary