1JW6

Crystal Structure of the Complex of Concanavalin A and Hexapeptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Crystal structure of the complex of concanavalin A and hexapeptide.

Zhang, Z.Qian, M.Huang, Q.Jia, Y.Tang, Y.Wang, K.Cui, D.Li, M.

(2001) J Protein Chem 20: 423-429

  • DOI: https://doi.org/10.1023/a:1012289022412
  • Primary Citation of Related Structures:  
    1JW6

  • PubMed Abstract: 

    The X-ray structure analysis of a cross-linked crystal of concanavalin A soaked with a hexapeptide molecule as a probe molecule showed an electron density corresponding to full occupation in the binding pocket. The site lies on the surface of concanavalin A and is surrounded by three symmetry-related molecules. The crystal structure of the hexapeptide complex was refined at 1.93-A resolution, to an R-factor of 19% (Rfree factor of 25%), with an RMS deviation in bond distances of 0.01 A. The model includes all 237 residues of concanavalin A, one manganese ion, one calcium ion, 95 water molecules, one glutaraldehyde molecule, one isopropanol molecule, and one hexapeptide molecule. This X-ray structure analysis also provides an approach to mapping the binding surface of crystalline protein with a probe molecule that is dissolved in the mixture of organic solvent with water or in neat organic solvent but is hardly dissolved in aqueous solution.


  • Organizational Affiliation

    Department of Chemistry, Peking University, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Concanavalin A237Canavalia ensiformisMutation(s): 0 
UniProt
Find proteins for P02866 (Canavalia ensiformis)
Explore P02866 
Go to UniProtKB:  P02866
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02866
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (6-MER)6synthetic constructMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.210 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.36α = 90
b = 86.38β = 90
c = 89.25γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-09-26
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-06-21
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.4: 2017-10-04
    Changes: Refinement description
  • Version 1.5: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description