4K21 | pdb_00004k21

Crystal structure of Canavalia boliviana lectin in complex with Xman


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.192 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.146 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 
    0.148 (Depositor) 

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Ligand Structure Quality Assessment 

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This is version 1.3 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: https://doi.org/10.1371/journal.pone.0097015
  • Primary Citation of Related Structures:  
    4K1Y, 4K1Z, 4K20, 4K21

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Canavalia boliviana lectin237Canavalia bolivianaMutation(s): 0 
UniProt
Find proteins for A0A023GPI8 (Canavalia boliviana)
Explore A0A023GPI8 
Go to UniProtKB:  A0A023GPI8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A023GPI8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.192 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.146 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 0.148 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.97α = 90
b = 66.59β = 90
c = 108.77γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted XMMClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-09
    Type: Initial release
  • Version 1.1: 2014-06-11
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Structure summary