6AHG

Trimeric structure of concanavalin A from Canavalia ensiformis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 2CTV - determined by Weisgerber, S., Helliwell, J.R.  

Literature

Cadmium-substituted concanavalin A and its trimeric complexation

Park, Y.R.Kim, D.S.Lee, D.H.Kang, H.G.Park, J.H.Lee, S.J.

(2018) J. Microbiol. Biotechnol. 28(12): 2106-2112

  • DOI: 10.4014/jmb.1809.09027

  • PubMed Abstract: 
  • Concanavalin A (ConA) interacts with carbohydrates as a lectin, and recent reports proposed its application for detecting a diversity of viruses and pathogens. Structural studies have detailed the interaction between ConA and carbohydrates and the me ...

    Concanavalin A (ConA) interacts with carbohydrates as a lectin, and recent reports proposed its application for detecting a diversity of viruses and pathogens. Structural studies have detailed the interaction between ConA and carbohydrates and the metal coordination environment with manganese and calcium ions (Mn-Ca-ConA). In this study, ConA was crystallized with a cadmium-containing precipitant, and the refined structure indicates that Mn²⁺ was replaced by Cd²⁺ (Cd-Ca-ConA). The structural comparison with ConA demonstrates that the metal-coordinated residues of Cd-Ca-ConA, that is Glu8, Asp10, Asn14, Asp19, and His24, do not have conformational shifts, but residues for sugar binding, including Arg228, Tyr100, and Leu99, reorient their side chains, slightly. Previous studies demonstrated that excess cadmium ions can coordinate with other residues, including Glu87 and Glu183, which were not coordinated with Cd²⁺ in this study. The trimeric ConA in this study coordinated Cd²⁺ with other residues, including Asp80 and Asp82, for the complex generation. The monomers does not have specific interaction near interface regions with the other monomer, but secondary cadmium coordinated with two aspartates (Asp80 and Asp82) from monomer 1 and one aspartate (Asp16) from monomer 2. This study demonstrated that complex generation was induced via coordination with secondary Cd²⁺ and showed the application potential regarding the design of complex formation for specific interactions with target saccharides.


    Organizational Affiliation

    Department of Chemistry and Institute for Molecular Biology and Genetics, Chonbuk National University, Jeonju 54896, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Concanavalin-A,Concanavalin-A
A, B, C
237Canavalia ensiformisMutation(s): 0 
Find proteins for P02866 (Canavalia ensiformis)
Go to UniProtKB:  P02866
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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

Download SDF File 
Download CCD File 
A, B, C
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.243 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 136.461α = 90.00
b = 136.461β = 90.00
c = 193.146γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Cootmodel building
SCALAdata scaling
HKL-2000data reduction
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education (Korea)Korea, Republic OfNRF-2017R1A6A1A03015876

Revision History 

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 1.1: 2019-01-16
    Type: Data collection, Database references