6Y7T

Engineered conjugation of lysine-specific molecular tweezers with ExoS derived peptidic inhibitor enhance affinity towards target protein 14-3-3 through ditopic binding


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Supramolecular Enhancement of a Natural 14-3-3 Protein Ligand.

Guillory, X.Hadrovic, I.de Vink, P.J.Sowislok, A.Brunsveld, L.Schrader, T.Ottmann, C.

(2021) J Am Chem Soc 143: 13495-13500

  • DOI: https://doi.org/10.1021/jacs.1c07095
  • Primary Citation of Related Structures:  
    6Y7T

  • PubMed Abstract: 

    Rational design of protein-protein interaction (PPI) inhibitors is challenging. Connecting a general supramolecular protein binder with a specific peptidic ligand provides a novel conceptual approach. Thus, lysine-specific molecular tweezers were conjugated to a peptide-based 14-3-3 ligand and produced a strong PPI inhibitor with 100-fold elevated protein affinity. X-ray crystal structure elucidation of this supramolecular directed assembly provides unique molecular insight into the binding mode and fully aligns with Molecular Dynamics (MD) simulations. This new supramolecular chemical biology concept opens the path to novel chemical tools for studying PPIs.


  • Organizational Affiliation

    Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular System, Eindhoven University of Technology, (TU/e) Den Dolech 2, 5612 AZ Eindhoven, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
14-3-3 protein sigmaA,
D [auth F],
E [auth K],
F [auth P]
253Homo sapiensMutation(s): 0 
Gene Names: SFNHME1
UniProt & NIH Common Fund Data Resources
Find proteins for P31947 (Homo sapiens)
Explore P31947 
Go to UniProtKB:  P31947
PHAROS:  P31947
GTEx:  ENSG00000175793 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31947
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Exoenzyme SB [auth D],
C [auth E]
11Pseudomonas aeruginosaMutation(s): 0 
UniProt
Find proteins for G3XDA1 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore G3XDA1 
Go to UniProtKB:  G3XDA1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG3XDA1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TWZ (Subject of Investigation/LOI)
Query on TWZ

Download Ideal Coordinates CCD File 
I [auth D],
J [auth E]
ExoSTWZ molecular tweezer
C48 H39 N3 O10 P2
GKFPJECGUVOTIP-LKPYISKYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A],
O [auth P]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
G [auth A],
K [auth F],
L [auth K],
M [auth P],
N [auth P]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A,
D [auth F],
E [auth K],
F [auth P]
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.151α = 90
b = 63.119β = 101.29
c = 167.021γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--
Netherlands Organisation for Scientific Research (NWO)Netherlands--

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-31
    Type: Initial release
  • Version 1.1: 2021-10-13
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Refinement description