1ONA

CO-CRYSTALS OF CONCANAVALIN A WITH METHYL-3,6-DI-O-(ALPHA-D-MANNOPYRANOSYL)-ALPHA-D-MANNOPYRANOSIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A structure of the complex between concanavalin A and methyl-3,6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranoside reveals two binding modes.

Loris, R.Maes, D.Poortmans, F.Wyns, L.Bouckaert, J.

(1996) J.Biol.Chem. 271: 30614-30618


  • PubMed Abstract: 
  • The structure of concanavalin A in complex with the trimannoside methyl-3,6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranoside has been determined in a novel space group. In three of the four subunits of the concanavalin A tetramer, the interactio ...

    The structure of concanavalin A in complex with the trimannoside methyl-3,6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranoside has been determined in a novel space group. In three of the four subunits of the concanavalin A tetramer, the interactions between the protein and the bound saccharide are essentially identical to those reported previously by other authors (Naismith, J. H., and Field, R. A. (1996) J. Biol. Chem. 271, 972-976). In the fourth subunit, however, the alpha1-->3 linkage has a different conformation, resulting in a different part of the alpha1-->3-linked mannose interacting with essentially the same surface of the protein. Furthermore, significant differences are observed in the quaternary associations of the subunits compared with the saccharide-free structures and other carbohydrate complexes, suggesting that the concanavalin A tetramer is a rather flexible entity.


    Related Citations: 
    • Structural Basis of Trimannoside Recognition by Concanavalin A
      Naismith, J.H.,Field, R.A.
      (1996) J.Biol.Chem. 271: 972
    • Concanavalin a Crystallized in Complex with the Trisaccharide 3,6-Di-O-(Alpha-D-Mannopyranosyl)-Alpha-D-Mannopyranoside
      Bouckaert, J.,Poortmans, F.,Wyns, L.
      (1996) Acta Crystallogr.,Sect.D 52: 879


    Organizational Affiliation

    Laboratorium voor Ultrastruktuur, Vlaams Interuniversitair Instituut voor Biotechnologie, Vrije Universiteit Brussel, Paardenstraat 65, B-1640 Sint-Genesius-Rode, Belgium. bouckaej@vub.ac.be




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CONCANAVALIN A
A, B, C, D
237Canavalia ensiformisN/A
Find proteins for P02866 (Canavalia ensiformis)
Go to UniProtKB:  P02866
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B, C, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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

Download SDF File 
Download CCD File 
A, B, C, D
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
MMA
Query on MMA

Download SDF File 
Download CCD File 
A, B, C, D
O1-METHYL-MANNOSE
C7 H14 O6
HOVAGTYPODGVJG-VEIUFWFVSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MAMIC50: 350000 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.221 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 59.830α = 90.00
b = 64.840β = 93.87
c = 125.920γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
CCP4data scaling
X-PLORmodel building
MADNESdata reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-09-17
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2016-02-17
    Type: Derived calculations, Non-polymer description