5FXC

Crystal structure of glycopeptide 22 in complex with scFv-SM3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Design of Alpha-S-Glycopeptides Derived from Muc1 with a Flexible and Solvent Exposed Sugar Moiety

Rojas-Ocariz, V.Companon, I.Aydillo, C.Castro-Lopez, J.Jimenez-Barbero, J.Hurtado-Guerrero, R.Avenoza, A.Zurbano, M.M.Corzana, F.Busto, J.H.Peregrina, J.M.

(2016) J Org Chem 81: 5929

  • DOI: https://doi.org/10.1021/acs.joc.6b00833
  • Primary Citation of Related Structures:  
    5FXC

  • PubMed Abstract: 

    The use of vaccines based on MUC1 glycopeptides is a promising approach to treat cancer. We present herein several sulfa-Tn antigens incorporated in MUC1 sequences that possess a variable linker between the carbohydrate (GalNAc) and the peptide backbone. The main conformations of these molecules in solution have been evaluated by combining NMR experiments and molecular dynamics simulations. The linker plays a key role in the modulation of the conformation of these compounds at different levels, blocking a direct contact between the sugar moiety and the backbone, promoting a helix-like conformation for the glycosylated residue and favoring the proper presentation of the sugar unit for molecular recognition events. The feasibility of these novel compounds as mimics of MUC1 antigens has been validated by the X-ray diffraction structure of one of these unnatural derivatives complexed to an anti-MUC1 monoclonal antibody. These features, together with potential lack of immune suppression, render these unnatural glycopeptides promising candidates for designing alternative therapeutic vaccines against cancer.


  • Organizational Affiliation

    Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja , Madre de Dios 53, 26006 Logroño, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SCFV-SM3A [auth H]244Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GLYCOPEPTIDEB [auth P]6Mus musculusMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.349α = 90
b = 67.875β = 90
c = 90.889γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-29
    Type: Initial release
  • Version 1.1: 2016-07-27
    Changes: Database references
  • Version 1.2: 2016-12-14
    Changes: Structure summary
  • Version 1.3: 2017-08-23
    Changes: Data collection
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description