4K21

Crystal structure of Canavalia boliviana lectin in complex with Xman


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.146 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Studies of an Anti-Inflammatory Lectin from Canavalia boliviana Seeds in Complex with Dimannosides.

Bezerra, G.A.Viertlmayr, R.Moura, T.R.Delatorre, P.Rocha, B.A.do Nascimento, K.S.Figueiredo, J.G.Bezerra, I.G.Teixeira, C.S.Simoes, R.C.Nagano, C.S.de Alencar, N.M.Gruber, K.Cavada, B.S.

(2014) Plos One 9: e97015-e97015

  • DOI: 10.1371/journal.pone.0097015
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Plant lectins, especially those purified from species of the Leguminosae family, represent the best-studied group of carbohydrate-binding proteins. Lectins purified from seeds of the Diocleinae subtribe exhibit a high degree of sequence identity notw ...

    Plant lectins, especially those purified from species of the Leguminosae family, represent the best-studied group of carbohydrate-binding proteins. Lectins purified from seeds of the Diocleinae subtribe exhibit a high degree of sequence identity notwithstanding that they show very distinct biological activities. Two main factors have been related to this feature: variance in key residues influencing the carbohydrate-binding site geometry and differences in the pH-dependent oligomeric state profile. In this work, we have isolated a lectin from Canavalia boliviana (Cbol) and solved its x-ray crystal structure in the unbound form and in complex with the carbohydrates Man(α1-3)Man(α1-O)Me, Man(α1-4)Man(α1-O)Me and 5-bromo-4-chloro-3-indolyl-α-D-mannose. We evaluated its oligomerization profile at different pH values using Small Angle X-ray Scattering and compared it to that of Concanavalin A. Based on predicted pKa-shifts of amino acids in the subunit interfaces we devised a model for the dimer-tetramer equilibrium phenomena of these proteins. Additionally, we demonstrated Cbol anti-inflammatory properties and further characterized them using in vivo and in vitro models.


    Organizational Affiliation

    Institute of Molecular Biosciences, University of Graz, Graz, Austria.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Canavalia boliviana lectin
A
237Canavalia bolivianaMutation(s): 0 
Find proteins for A0A023GPI8 (Canavalia boliviana)
Go to UniProtKB:  A0A023GPI8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
XMM
Query on XMM

Download SDF File 
Download CCD File 
A
(2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL
(5-BROMO-4-CHLORO-3-INDOLYL)-A-D-MANNOSE
C14 H15 Br Cl N O6
OPIFSICVWOWJMJ-HAAGFXOZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.146 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 64.970α = 90.00
b = 66.590β = 90.00
c = 108.770γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHASERphasing
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-09
    Type: Initial release
  • Version 1.1: 2014-06-11
    Type: Database references