1QDO

MAN(APLHA1-3)MAN(ALPHA1-O)METHYL CONCANAVALIN A COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.164 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

The crystal structures of Man(alpha1-3)Man(alpha1-O)Me and Man(alpha1-6)Man(alpha1-O)Me in complex with concanavalin A.

Bouckaert, J.Hamelryck, T.W.Wyns, L.Loris, R.

(1999) J Biol Chem 274: 29188-29195

  • DOI: 10.1074/jbc.274.41.29188
  • Primary Citation of Related Structures:  
    1QDC, 1QDO

  • PubMed Abstract: 
  • The crystal structures of concanavalin A in complex with Man(alpha1-6)Man(alpha1-O)Me and Man(alpha1-3)Man(alpha1-O)Me were determined at resolutions of 2.0 and 2.8 A, respectively. In both structures, the O-1-linked mannose binds in the conserved monosaccharide-binding site ...

    The crystal structures of concanavalin A in complex with Man(alpha1-6)Man(alpha1-O)Me and Man(alpha1-3)Man(alpha1-O)Me were determined at resolutions of 2.0 and 2.8 A, respectively. In both structures, the O-1-linked mannose binds in the conserved monosaccharide-binding site. The O-3-linked mannose of Man(alpha1-3)Man(alpha1-O)Me binds in the hydrophobic subsite formed by Tyr-12, Tyr-100, and Leu-99. The shielding of a hydrophobic surface is consistent with the associated large heat capacity change. The O-6-linked mannose of Man(alpha1-6)Man(alpha1-O)Me binds in the same subsite formed by Tyr-12 and Asp-16 as the reducing mannose of the highly specific trimannose Man(alpha1-3)[Man(alpha1-6)]Man(alpha1-O)Me. However, it is much less tightly bound. Its O-2 hydroxyl makes no hydrogen bond with the conserved water 1. Water 1 is present in all the sugar-containing concanavalin A structures and increases the complementarity between the protein-binding surface and the sugar, but is not necessarily a hydrogen-bonding partner. A water analysis of the carbohydrate-binding site revealed a conserved water molecule replacing O-4 on the alpha1-3-linked arm of the trimannose. No such water is found for the reducing or O-6-linked mannose. Our data indicate that the central mannose of Man(alpha1-3)[Man(alpha1-6)]Man(alpha1-O)Me primarily functions as a hinge between the two outer subsites.


    Related Citations: 
    • Concanavalin a Crystallized in Complex with the Trisaccharide 3,6-Di-O-(Alpha-D-Mannopyranosyl)-Alpha-D-Mannopyranoside
      Loris, R., Maes, D., Poortmans, F., Wyns, L., Bouckaert, J.
      (1996) J Biol Chem 271: 30614
    • Structural Basis of Trimannoside Recognition by Concanavalin A
      Naismith, J.H., Field, R.A.
      (1996) J Biol Chem 271: 972
    • Thermodynamics of Lectin-Carbohydrate Interactions. Titration Microcalorimetry Measurements of the Binding of N-Linked Carbohydrates and Ovalbumin to Concanavalin A
      Mandal, D.K., Kishore, N., Brewer, C.F.
      (1994) Biochemistry 33: 1149

    Organizational Affiliation

    Laboratorium voor Ultrastructuur, 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (CONCANAVALIN A)A, B, C, D237Canavalia ensiformisMutation(s): 0 
UniProt
Find proteins for P55915 (Canavalia brasiliensis)
Explore P55915 
Go to UniProtKB:  P55915
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-methyl alpha-D-mannopyranosideE, F, G, H2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G59594NN
GlyCosmos:  G59594NN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.164 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.41α = 90
b = 64.53β = 93.21
c = 126.96γ = 90
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-10-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary