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 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • 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

    Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Bijvoet Center for Biomolecular Research, Utrecht University , Universiteitsweg 99, Utrecht, The Netherlands.,(i) CIC bioGUNE, Bizkaia Technology Park, Building 801A, 48170 Derio, Spain; (ii) Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 13, 48009 Bilbao, Spain; (iii) Department of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country , 48940 Leioa, Spain.,Instituto de Medicina Molecular, Faculdade de Medicina da, Universidade de Lisboa , Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal.,Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, BIFI-IQFR (CSIC) , Zaragoza, Spain.,Graduate School and Faculty of Advanced Life Science, Field of Drug Discovery Research, Hokkaido University , N21 W11, Sapporo 001-0021, Japan.,Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química , 26006 Logroño, Spain.,Instituto de Química Orgánica General, IQOG-CSIC , 28006 Madrid, Spain.,Fundación ARAID , 50018 Zaragoza, Spain.,Department of Chemistry, University of Cambridge , Lensfield Road, CB2 1EW Cambridge, U.K.




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 H2020
H
244N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE
D
8N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
H
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
A2G
Query on A2G

Download SDF File 
Download CCD File 
D
N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
C8 H15 N O6
OVRNDRQMDRJTHS-CBQIKETKSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
4FB
Query on 4FB
D
L-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 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 35.399α = 90.00
b = 68.151β = 90.00
c = 90.358γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2017-12-27
    Type: Database references