Skip to main content

 4K1Z | pdb_00004k1z

Crystal structure of Canavalia boliviana lectin in complex with Man1-4Man-OMe


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.222 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.161 (Depositor), 0.159 (DCC) 
  • R-Value Observed: 
    0.164 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4K1Z

This is version 2.1 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: https://doi.org/10.1371/journal.pone.0097015
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 105.27 kDa 
  • Atom Count: 7,881 
  • Modeled Residue Count: 948 
  • Deposited Residue Count: 948 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Canavalia boliviana lectin
A, B, C, D
237Canavalia 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

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-4)-methyl alpha-D-mannopyranoside
E, F, G, H
2N/A
Glycosylation Resources
GlyTouCan: G81519SA
GlyCosmos: G81519SA

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CD

Query on CD



Download:Ideal Coordinates CCD File
AA [auth D]
K [auth A]
L [auth A]
M [auth A]
N [auth A]
AA [auth D],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
Q [auth B],
R [auth B],
W [auth C],
Z [auth D]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
MN

Query on MN



Download:Ideal Coordinates CCD File
I [auth A],
O [auth B],
U [auth C],
X [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
J [auth A],
P [auth B],
V [auth C],
Y [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
S [auth B],
T [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.222 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.161 (Depositor), 0.159 (DCC) 
  • R-Value Observed: 0.164 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.81α = 90
b = 107.81β = 90
c = 157.91γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

View Full Validation Report



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 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-02-28
    Changes: Data collection, Database references, Structure summary