4NCW

foldon domain wild type C-conjugate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Versatile C(3)-symmetric scaffolds and their use for covalent stabilization of the foldon trimer.

Berthelmann, A.Lach, J.Grawert, M.A.Groll, M.Eichler, J.

(2014) Org Biomol Chem 12: 2606-2614

  • DOI: https://doi.org/10.1039/c3ob42251h
  • Primary Citation of Related Structures:  
    4NCU, 4NCV, 4NCW

  • PubMed Abstract: 

    C3-Symmetric trimesic acid scaffolds, functionalized with bromoacetyl, aminooxyacetyl and azidoacetyl moieties, respectively, were synthesized and compared regarding their utility for the trivalent presentation of peptides using three different chemoselective ligation reactions, i.e. thioether and oxime formation, as well as the "click" reaction. The latter ligation method was then used to covalently stabilize the trimer of foldon, a 27 amino acid trimerization domain of bacteriophage T4 fibritin, by linking the three foldon monomers to the triazido-functionalized trimesic acid scaffold. This reaction dramatically enhanced the thermal stability of the trimer, while maintaining the correct fold, as demonstrated by CD spectroscopy and X-ray crystal structure analysis, respectively, of the foldon-scaffold conjugates.


  • Organizational Affiliation

    Department of Chemistry and Pharmacy, University of Erlangen-Nurnberg, Schuhstr. 19, 91052 Erlangen, Germany. jutta.eichler@fau.de.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fibritin
A, B, C
27Tequatrovirus T4Mutation(s): 0 
UniProt
Find proteins for P10104 (Enterobacteria phage T4)
Explore P10104 
Go to UniProtKB:  P10104
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10104
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2KN
Query on 2KN

Download Ideal Coordinates CCD File 
D [auth B]N,N',N''-triethylbenzene-1,3,5-tricarboxamide
C15 H21 N3 O3
OHEQFYRYAKNXEC-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.71α = 90
b = 28.1β = 106.81
c = 55.99γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-12
    Type: Initial release
  • Version 1.1: 2014-10-08
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description