6TNP | pdb_00006tnp

Crystal structure of the ScFv-5E5 in complex with a Tn glycopeptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.251 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history. 

Literature

Structural characterization of an unprecedented lectin-like antitumoral anti-MUC1 antibody.

Macias-Leon, J., Bermejo, I.A., Asin, A., Garcia-Garcia, A., Companon, I., Jimenez-Moreno, E., Coelho, H., Mangini, V., Albuquerque, I.S., Marcelo, F., Asensio, J.L., Bernardes, G.J.L., Joshi, H.J., Fiammengo, R., Blixt, O., Hurtado-Guerrero, R., Corzana, F.

(2020) Chem Commun (Camb) 56: 15137-15140

  • DOI: https://doi.org/10.1039/d0cc06349e
  • Primary Citation Related Structures: 
    6TNP

  • PubMed Abstract: 

    The molecular basis of antibody 5E5, which recognizes the entire GalNAc unit as a primary epitope is disclosed. The antibody's contacts with the peptide are mostly limited to two residues, allowing it to show some degree of promiscuity. These findings open the door to the chemical design of peptide-mimetics for developing efficient anti-cancer vaccines and diagnostic tools.

    • Organizational Affiliation: 
    • Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, Spain. rhurtado@bifi.es.

Macromolecule Content 

  • Total Structure Weight: 156.14 kDa 
  • Atom Count: 10,657 
  • Modeled Residue Count: 1,342 
  • Deposited Residue Count: 1,374 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Light chain of our ScFv-5E5
A, C, E, G, J
A, C, E, G, J, L
113Mus musculusMutation(s): 0 
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Heavy chain of our ScFv-5E5
B, D, F, H, I
B, D, F, H, I, K
116Mus musculusMutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NO8
(Subject of Investigation/LOI)

Query on NO8


Download:Ideal Coordinates CCD File
M [auth B],
N [auth D],
O [auth F],
P [auth H],
Q [auth I]		(2~{S})-~{N}-[2-[[(2~{S})-1-[[(2~{S},3~{R})-3-[(2~{S},3~{R},4~{R},5~{R},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-1-[[(2~{S})-1-[(2~{S})-2-aminocarbonylpyrrolidin-1-yl]-1-oxidanylidene-propan-2-yl]amino]-1-oxidanylidene-butan-2-yl]amino]-3-oxidanyl-1-oxidanylidene-propan-2-yl]amino]-2-oxidanylidene-ethyl]-1-[(2~{S})-2-azanylpropanoyl]pyrrolidine-2-carboxamide
C33 H55 N9 O14
SQMBDAVTEXMIPT-PEECNIKTSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.251 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.573α = 90
b = 113.195β = 90
c = 151.201γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-18
    Type: Initial release
  • Version 1.1: 2020-12-02
    Changes: Database references
  • Version 1.2: 2020-12-16
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary