2DVA

Crystal structure of peanut lectin GAL-BETA-1,3-GALNAC-ALPHA-O-ME (Methyl-T-antigen) complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structural studies on peanut lectin complexed with disaccharides involving different linkages: further insights into the structure and interactions of the lectin

Natchiar, S.K.Srinivas, O.Mitra, N.Surolia, A.Jayaraman, N.Vijayan, M.

(2006) Acta Crystallogr D Biol Crystallogr 62: 1413-1421

  • DOI: 10.1107/S0907444906035712
  • Primary Citation of Related Structures:  
    2DV9, 2DVA, 2DVB, 2DVD, 2DVF, 2DVG

  • PubMed Abstract: 
  • Crystal structures of peanut lectin complexed with Galbeta1-3Gal, methyl-T-antigen, Galbeta1-6GalNAc, Galalpha1-3Gal and Galalpha1-6Glc and that of a crystal grown in the presence of Galalpha1-3Galbeta1-4Gal have been determined using data collected at 100 K ...

    Crystal structures of peanut lectin complexed with Galbeta1-3Gal, methyl-T-antigen, Galbeta1-6GalNAc, Galalpha1-3Gal and Galalpha1-6Glc and that of a crystal grown in the presence of Galalpha1-3Galbeta1-4Gal have been determined using data collected at 100 K. The use of water bridges as a strategy for generating carbohydrate specificity was previously deduced from the complexes of the lectin with lactose (Galbeta1-4Glc) and T-antigen (Galbeta1-3GalNAc). This has been confirmed by the analysis of the complexes with Galbeta1-3Gal and methyl-T-antigen (Galbeta1-3GalNAc-alpha-OMe). A detailed analysis of lectin-sugar interactions in the complexes shows that they are more extensive when the beta-anomer is involved in the linkage. As expected, the second sugar residue is ill-defined when the linkage is 1-->6. There are more than two dozen water molecules which occur in the hydration shells of all structures determined at resolutions better than 2.5 A. Most of them are involved in stabilizing the structure, particularly loops. Water molecules involved in lectin-sugar interactions are also substantially conserved. The lectin molecule is fairly rigid and does not appear to be affected by changes in temperature.


    Related Citations: 
    • Crystal structure of peanut lectin, a protein with an unusual quaternary structure
      Banerjee, R., Mande, S.C., Ganesh, V., Das, K., Dhanaraj, V., Mahanta, S.K., Suguna, K., Surolia, A., Vijayan, M.
      (1994) Proc Natl Acad Sci U S A 91: 227
    • Conformation, protein-carbohydrate interactions and a novel subunit association in the refined structure of peanut lectin-lactose complex
      Banerjee, R., Das, K., Ravishankar, R., Suguna, K., Surolia, A., Vijayan, M.
      (1996) J Mol Biol 259: 281
    • The Specificity of Peanut Agglutinin for Thomsen-Friedenreich Antigen is Mediated by Water-Bridges
      Ravishankar, R., Ravindran, M., Suguna, K., Surolia, A., Vijayan, M.
      (1997) Curr Sci 72: 855
    • Structural plasticity of peanut lectin: an X-ray analysis involving variation in pH, ligand binding and crystal structure
      Natchiar, S.K., Jeyaprakash, A.A., Ramya, T.N., Thomas, C.J., Suguna, K., Surolia, A., Vijayan, M.
      (2004) Acta Crystallogr D Biol Crystallogr 60: 211
    • Multivalency in Lectins. A Crystallographic Modellin and Light-Scattering Study Involving Peanut Lectin and a Bivalent Ligand
      Natchiar, S.K., Srinivas, O., Nivedita, M., Sagarika, D., Jayaraman, N., Surolia, A., Vijayan, M.
      (2006) Curr Sci 90: 1230

    Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Galactose-binding lectinA, B, C, D236Arachis hypogaeaMutation(s): 0 
UniProt
Find proteins for P02872 (Arachis hypogaea)
Explore P02872 
Go to UniProtKB:  P02872
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-galactopyranose-(1-3)-methyl 2-acetamido-2-deoxy-alpha-D-galactopyranosideE, F, G, H2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G70497XY
GlyCosmos:  G70497XY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.59α = 90
b = 124.62β = 90
c = 75.78γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-11-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    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: Advisory, Atomic model, Data collection, Derived calculations, Structure summary