4K21

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 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.148 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XMM
Query on XMM

Download Ideal Coordinates CCD File 
D [auth A]5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside
C14 H15 Br Cl N O6
OPIFSICVWOWJMJ-HAAGFXOZSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
B [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.148 
  • 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 


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