1CVN

CONCANAVALIN A COMPLEXED TO TRIMANNOSIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 

wwPDB Validation 3D Report Full Report



Literature

Structural basis of trimannoside recognition by concanavalin A.

Naismith, J.H.Field, R.A.

(1996) J Biol Chem 271: 972-976

  • DOI: 10.1074/jbc.271.2.972
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Despite the fact that complex saccharides play an important role in many biological recognition processes, molecular level descriptions of protein-carbohydrate interactions are sparse. The legume lectin concanavalin A (con A), from Canavalia ensiform ...

    Despite the fact that complex saccharides play an important role in many biological recognition processes, molecular level descriptions of protein-carbohydrate interactions are sparse. The legume lectin concanavalin A (con A), from Canavalia ensiformis, specifically recognizes the trimannoside core of many complex glycans. We have determined the crystal structure of a con A-trimannoside complex at 2.3-A resolution now describe the trimannoside interaction with conA. All three sugar residues are in well defined difference electron density. The 1,6-linked mannose residue is bound at the previously reported monosaccharide binding site; the other two sugars bind in an extended cleft formed by residues Tyr-12, Pro-13, Asn-14, Thr-15, and Asp-16. Hydrogen bonds are formed between the protein and all three sugar residues. In particular, the 1,3-linked mannose residue makes a strong hydrogen bond with the main chain of the protein. In addition, a water molecule, which is conserved in other con A structures, plays an important role in anchoring the reducing sugar unit to the protein. The complex is further stabilized by van der Waals interactions. The structure provides a rationale for the high affinity of con A for N-linked glycans.


    Related Citations: 
    • Refined Structure of Concanavalin a Complexed with Methyl Alpha-D-Mannopyranoside at 2.0A Resolution and Comparison with the Saccharide-Free Structure
      Naismith, J.H., Emmerich, C., Habash, J., Harrop, S.J., Helliwell, J.R., Hunter, W.N., Raftery, J., Kalb(Gilboa), A.J., Yariv, J.
      (1994) Acta Crystallogr D Biol Crystallogr 50: 847
    • Refined Structure of Cadmium-Substituted Concanavalin a at 2.0A Resolution
      Naismith, J.H., Habash, J., Harrop, S.J., Helliwell, J.R., Hunter, W.N., Wan, T.C.M., Weisgerber, S., Kalb(Gilboa), A.J., Yariv, J.
      (1993) Acta Crystallogr D Biol Crystallogr 49: 561

    Organizational Affiliation

    Centre for Biomolecular Sciences, University, St. Andrews, Scotland, United Kingdom.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CONCANAVALIN AA, B, C, D237Canavalia ensiformisMutation(s): 0 
Find proteins for P02866 (Canavalia ensiformis)
Explore P02866 
Go to UniProtKB:  P02866
Protein Feature View
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  • Reference Sequence
Oligosaccharides
Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose
E, F, G, H
3 N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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

Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.65α = 90
b = 66.68β = 97.79
c = 108.32γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 1995-08-09 
  • Released Date: 1996-10-14 
  • Deposition Author(s): Naismith, J.H.

Revision History 

  • Version 1.0: 1996-10-14
    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: 2018-04-18
    Changes: Advisory, Data collection, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary