1N47

Isolectin B4 from Vicia villosa in complex with the Tn antigen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of a plant lectin in complex with the Tn antigen

Babino, A.Tello, D.Rojas, A.Bay, S.Osinaga, E.Alzari, P.M.

(2003) FEBS Lett. 536: 106-110


  • PubMed Abstract: 
  • The structure of the tetrameric Vicia villosa isolectin B4 (VVLB4) in complex with a cancer antigen, the Tn glycopeptide (GalNAc-O-Ser), was determined at 2.7 A resolution. The N-acetylgalactoside moiety of the ligand binds to the primary combining s ...

    The structure of the tetrameric Vicia villosa isolectin B4 (VVLB4) in complex with a cancer antigen, the Tn glycopeptide (GalNAc-O-Ser), was determined at 2.7 A resolution. The N-acetylgalactoside moiety of the ligand binds to the primary combining site of VVLB4 in a similar way as observed for other Gal/GalNAc-specific plant lectins. The amino acid moiety of the Tn antigen is largely exposed to the solvent and makes few contacts with the protein. The structure of the complex provides a framework to understand the differences in the strength of VVLB4 binding to different sugars and emphasizes the role of a single protein residue, Tyr127, as a structural determinant of Tn-binding specificity.


    Related Citations: 
    • Amino acid sequence and three-dimensional structure of the Tn-specific isolectin B4 from Vicia villosa.
      Osinaga, E.,Tello, D.,Batthyany, C.,Bianchet, M.,Tavares, G.,Duran, R.,Cervenansky, C.,Camoin, L.,Roseto, A.,Alzari, P.M.
      (1997) FEBS Lett. 412: 190


    Organizational Affiliation

    Departamento de Bioquimica, Facultad de Medicina, Av. Gral Flores 2125, Montevideo, Uruguay.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Isolectin B4
A, B, C, D
233Vicia villosaN/A
Find proteins for P56625 (Vicia villosa)
Go to UniProtKB:  P56625
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B, C, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
TNR
Query on TNR

Download SDF File 
Download CCD File 
A, B, C, D
O-(2-ACETAMIDO-2-DEOXY-ALPHA-D-GALACTOPYRANOSYL)-L-SERINE
C11 H20 N2 O8
REDMNGDGDYFZRE-WKWISIMFSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
A, B, C, D
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.188 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 85.510α = 90.00
b = 85.510β = 90.00
c = 153.650γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-02-25
    Type: Initial release
  • Version 1.1: 2008-04-02
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance