5YGM

Monomeric structure of concanavalin A at pH 7.5 from Carnivalia ensiformis

• PDB DOI: https://doi.org/10.2210/pdb5YGM/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Canavalia ensiformis
• Expression System: Canavalia ensiformis
• Mutation(s): No 


• Deposited: 2017-09-24 Released: 2017-10-25 
• Deposition Author(s): Park, J.H., Park, Y.R., Lee, S.J.
• Funding Organization(s): Cooperative Research Program for Agriculture Science and Technology Development Rural Development Administration

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.196 
• R-Value Work: 0.166 
• R-Value Observed: 0.167 

Starting Model: experimental

Literature

Heterometal-Coordinated Monomeric Concanavalin A at pH 7.5 from Canavalia ensiformis

Chung, N.J., Park, Y.R., Lee, D.H., Oh, S.Y., Park, J.H., Lee, S.J.

(2017) J Microbiol Biotechnol 27: 2241-2244

• PubMed: 29025256 
• DOI: https://doi.org/10.4014/jmb.1709.09057
• Primary Citation of Related Structures:  
  5YGM


• PubMed Abstract: 
  

  The structure of concanavalin A (ConA) has been studied intensively owing to its specific interactions with carbohydrates and its heterometal (Ca²⁺ and Mn²⁺) coordination. Most structures from X-ray crystallography have shown ConA as a dimer or tetramer, because the complex formation requires specific crystallization conditions. Here, we reported the monomeric structure of ConA with a resolution of 1.6 Å, which revealed that metal coordination could trigger sugar-binding ability. The calcium coordination residue, Asn14, changed the orientation of carbohydrate-binding residues and biophysical details, including structural information, providing valuable clues for the development and application of detection kits using ConA.

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Organizational Affiliation: 

Department of Crop Science and Biotechnology, Chonbuk National University, Jeonju 54896, Republic of Korea.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 25.72 kDa 
• Atom Count: 2,078 
• Modelled Residue Count: 237 
• Deposited Residue Count: 237 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Concanavalin-A	A	237	Canavalia ensiformis	Mutation(s): 0
UniProt
Find proteins for P55915 (Canavalia brasiliensis) Explore P55915  Go to UniProtKB:  P55915

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.196 
• R-Value Work: 0.166 
• R-Value Observed: 0.167 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.303	α = 90
b = 86.59	β = 90
c = 89.511	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data processing
SCALA	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-10-25 
Deposition Author(s): Park, J.H., Park, Y.R., Lee, S.J.

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Funding Organization	Location	Grant Number
Cooperative Research Program for Agriculture Science and Technology Development Rural Development Administration	Korea, Republic Of	PJ011067

Revision History  

• Version 1.0: 2017-10-25
  Type: Initial release
  
• Version 1.1: 2018-01-17
  Changes: Database references
• Version 1.2: 2018-08-01
  Changes: Data collection, Source and taxonomy, Structure summary
• Version 1.3: 2018-08-15
  Changes: Data collection, Database references, Source and taxonomy, Structure summary
• Version 1.4: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description