1CJP

CONCANAVALIN A COMPLEX WITH 4'-METHYLUMBELLIFERYL-ALPHA-D-GLUCOPYRANOSIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The crystal structure of the complex of concanavalin A with 4'-methylumbelliferyl-alpha-D-glucopyranoside.

Hamodrakas, S.J.Kanellopoulos, P.N.Pavlou, K.Tucker, P.A.

(1997) J Struct Biol 118: 23-30

  • DOI: https://doi.org/10.1006/jsbi.1996.3837
  • Primary Citation of Related Structures:  
    1CJP

  • PubMed Abstract: 

    Concanavalin A (Con A) is the best known plant lectin, with important biological properties arising from its specific saccharide-binding ability. Its exact biological role still remains unknown. The complex of Con A with 4'-methylumbelliferyl-alpha-D-glucopyranoside (alpha-MUG) has been crystallized in space group P2(1) with cell dimensions a = 81.62 A, b = 128.71 A, c = 82.23 A, and beta = 118.47 degrees. X-ray diffraction intensities to 2.78 A have been collected. The structure of the complex was solved by molecular replacement and refined by simulated annealing methods to a crystallographic R-factor value of 0.182 and a free-R-factor value of 0.216. The asymmetric unit contains four subunits arranged as a tetramer, with approximate 222 symmetry. A saccharide molecule is bound in the sugar-binding site at the surface of each subunit, with the nonsugar (aglycon) part adopting a different orientation in each subunit. The aglycon orientation, although probably determined by packing of tetramers in the crystal lattice, helps to characterize the orientation of the saccharide in the sugar-binding pocket. The structure is the best determined alpha-D-glucoside:Con A complex to date and the hydrogen bonding network in the saccharide-binding site can be described with some confidence and compared with that of the alpha-D-mannosides.


  • Organizational Affiliation

    Department of Biology, Section of Cell Biology and Biophysics, University of Athens, Panepistimiopolis, Greece.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CONCANAVALIN A
A, B, C, D
237Canavalia 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
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MUG
Query on MUG

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C],
N [auth D]
4-METHYLUMBELLIFERYL-ALPHA-D-GLUCOSE
C16 H18 O8
YUDPTGPSBJVHCN-JZYAIQKZSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C],
O [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
M [auth C],
P [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.62α = 90
b = 128.71β = 118.47
c = 82.23γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-10-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-09
    Changes: Database references, Derived calculations, Other, Refinement description