5OWP

Crystal structure of glycopeptide "GVTSAfPDT*RPAP" in complex with scFv-SM3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

wwPDB Validation 3D Report Full Report



Literature

The Use of Fluoroproline in MUC1 Antigen Enables Efficient Detection of Antibodies in Patients with Prostate Cancer.

Somovilla, V.J.Bermejo, I.A.Albuquerque, I.S.Martinez-Saez, N.Castro-Lopez, J.Garcia-Martin, F.Companon, I.Hinou, H.Nishimura, S.I.Jimenez-Barbero, J.Asensio, J.L.Avenoza, A.Busto, J.H.Hurtado-Guerrero, R.Peregrina, J.M.Bernardes, G.J.L.Corzana, F.

(2017) J Am Chem Soc 139: 18255-18261

  • DOI: 10.1021/jacs.7b09447
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • A structure-based design of a new generation of tumor-associated glycopeptides with improved affinity against two anti-MUC1 antibodies is described. These unique antigens feature a fluorinated proline residue, such as a (4S)-4-fluoro-l-proline or 4,4 ...

    A structure-based design of a new generation of tumor-associated glycopeptides with improved affinity against two anti-MUC1 antibodies is described. These unique antigens feature a fluorinated proline residue, such as a (4S)-4-fluoro-l-proline or 4,4-difluoro-l-proline, at the most immunogenic domain. Binding assays using biolayer interferometry reveal 3-fold to 10-fold affinity improvement with respect to the natural (glyco)peptides. According to X-ray crystallography and MD simulations, the fluorinated residues stabilize the antigen-antibody complex by enhancing key CH/π interactions. Interestingly, a notable improvement in detection of cancer-associated anti-MUC1 antibodies from serum of patients with prostate cancer is achieved with the non-natural antigens, which proves that these derivatives can be considered better diagnostic tools than the natural antigen for prostate cancer.


    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ig heavy chain V-III region J606,Ig lambda-1 chain V region H2020H244Mus musculusMutation(s): 0 
Find proteins for P01726 (Mus musculus)
Explore P01726 
Go to UniProtKB:  P01726
Find proteins for P01801 (Mus musculus)
Explore P01801 
Go to UniProtKB:  P01801
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINED8synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A2G
Query on A2G

Download CCD File 
D
2-acetamido-2-deoxy-alpha-D-galactopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-CBQIKETKSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
H
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
4FB
Query on 4FB
DL-PEPTIDE LINKINGC5 H8 F N O2PRO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.399α = 90
b = 68.151β = 90
c = 90.358γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Revision History 

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2017-12-27
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary