5NF0 | pdb_00005nf0

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

• PDB DOI: https://doi.org/10.2210/pdb5NF0/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Pseudomonas aeruginosa, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-03-13 Released: 2017-09-13 
• Deposition Author(s): Reymond, J.-L., Darbre, T., Stocker, A., Hong, W., van Delden, C., Koehler, T., Luscher, A., Visini, R., Fu, Y., Di Bonaventura, I., He, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free: 
  0.184 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

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, B.H., Fu, Y., Probst, D., Luscher, A., Kohler, T., van Delden, C., Stocker, A., Hong, W., Darbre, T., Reymond, J.L.

(2017) Chem Sci 8: 7464-7475

• PubMed: 29163899 
• DOI: https://doi.org/10.1039/c7sc01599b
• Primary Citation Related Structures: 
  5NES, 5NEY, 5NF0


• PubMed Abstract: 
  

  Here we report a new family of cyclic antimicrobial peptides (CAMPs) targeting MDR strains of Pseudomonas aeruginosa . These CAMPs are cyclized via a xylene double thioether bridge connecting two cysteines placed at the ends of a linear amphiphilic alternating d,l-sequence composed of lysines and tryptophans. Investigations by transmission electron microscopy (TEM), dynamic light scattering and atomic force microscopy (AFM) suggest that these peptide macrocycles interact with the membrane to form lipid-peptide aggregates. Amphiphilic conformations compatible with membrane disruption are observed in high resolution X-ray crystal structures of fucosylated derivatives in complex with lectin LecB. The potential for optimization is highlighted by N -methylation of backbone amides leading to derivatives with similar antimicrobial activity but lower hemolysis.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland . Email: [e-mail].
Department of Microbiology and Molecular Medicine , University of Geneva , Service of Infectious Diseases , University Hospital of Geneva , Geneva , Switzerland.
State Key Laboratory of Physical Chemistry of Solid Surfaces , College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 53.54 kDa 
• Atom Count: 4,303 
• Modeled Residue Count: 493 
• Deposited Residue Count: 497 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucose-binding lectin II (PA-IIL)	A, B, C, D	114	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: lecB, PAERUG_E15_London_28_01_14_00983, PAERUG_P32_London_17_VIM_2_10_11_00423, PAMH19_1713
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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CYD-TRP-TRD-LYS-LYD-LYS-LYD-LYS-TRD-TRP-CYD-GLY	E, G, H	12	synthetic construct	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fragment of ligand	F	5	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZDC	Q [auth E], S [auth F], T [auth G], V [auth H]	3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid C8 H14 O6 YTZUDUWVQZSKNN-OASCRQMUSA-N
OXE	R [auth E], U [auth G], W [auth H]	ORTHO-XYLENE C8 H10 CTQNGGLPUBDAKN-UHFFFAOYSA-N
CA	I [auth A], J [auth A], K [auth B], L [auth B], M [auth C], N [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:  0.184 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.278	α = 90
b = 99.966	β = 90
c = 106.611	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-09-13 
Deposition Author(s): Reymond, J.-L., Darbre, T., Stocker, A., Hong, W., van Delden, C., Koehler, T., Luscher, A., Visini, R., Fu, Y., Di Bonaventura, I., He, R.

Revision History  

• Version 1.0: 2017-09-13
  Type: Initial release
  
• Version 1.1: 2017-12-06
  Changes: Database references, Derived calculations
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 2.0: 2025-10-01
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary