1CVN

CONCANAVALIN A COMPLEXED TO TRIMANNOSIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis of trimannoside recognition by concanavalin A.

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

(1996) J.Biol.Chem. 271: 972-976

  • Also Cited By: 3D4K

  • 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 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.,Sect.D 49: 561
    • 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.,Sect.D 50: 847


    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 A
A, B, C, D
237Canavalia ensiformisMutation(s): 0 
Find proteins for P02866 (Canavalia ensiformis)
Go to UniProtKB:  P02866
Small Molecules
Ligands 3 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 81.650α = 90.00
b = 66.680β = 97.79
c = 108.320γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
X-PLORmodel building
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-04-18
    Type: Advisory, Data collection, Other