1UGX

Crystal structure of jacalin- Me-alpha-T-antigen (Gal-beta(1-3)-GalNAc-alpha-o-Me) complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Basis of the Carbohydrate Specificities of Jacalin: An X-ray and Modeling Study

Jeyaprakash, A.A.Katiyar, S.Swaminathan, C.P.Sekar, K.Surolia, A.Vijayan, M.

(2003) J.MOL.BIOL. 332: 217-228

  • Primary Citation of Related Structures:  
  • Also Cited By: 4R6R, 4R6Q, 4R6P, 4R6O, 4R6N, 1WS5, 1WS4, 1VBP, 1VBO

  • PubMed Abstract: 
  • The structures of the complexes of tetrameric jacalin with Gal, Me-alpha-GalNAc, Me-alpha-T-antigen, GalNAcbeta1-3Gal-alpha-O-Me and Galalpha1-6Glc (mellibiose) show that the sugar-binding site of jacalin has three components: the primary site, secon ...

    The structures of the complexes of tetrameric jacalin with Gal, Me-alpha-GalNAc, Me-alpha-T-antigen, GalNAcbeta1-3Gal-alpha-O-Me and Galalpha1-6Glc (mellibiose) show that the sugar-binding site of jacalin has three components: the primary site, secondary site A, and secondary site B. In these structures and in the two structures reported earlier, Gal or GalNAc occupy the primary site with the anomeric carbon pointing towards secondary site A. The alpha-substituents, when present, interact, primarily hydrophobically, with secondary site A which has variable geometry. O-H..., centered pi and C-H...pi hydrogen bonds involving this site also exist. On the other hand, beta-substitution leads to severe steric clashes. Therefore, in complexes involving beta-linked disaccharides, the reducing sugar binds at the primary site with the non-reducing end located at secondary site B. The interactions at secondary site B are primarily through water bridges. Thus, the nature of the linkage determines the mode of the association of the sugar with jacalin. The interactions observed in the crystal structures and modeling based on them provide a satisfactory qualitative explanation of the available thermodynamic data on jacalin-carbohydrate interactions. They also lead to fresh insights into the nature of the binding of glycoproteins by jacalin.


    Related Citations: 
    • Crystal structure of the jacalin-T-antigen complex and a comparative study of lectin-T-antigen complexes
      Jeyaprakash, A.A.,Rani, P.G.,Reddy, G.B.,Banumathi, S.,Betzel, C.,Sekar, K.,Surolia, A.,Vijayan, M.
      (2002) J.Mol.Biol. 321: 637
    • A novel mode of carbohydrate recognition in jacalin, a Moraceae plant lectin with a beta-prism fold
      Sankaranarayanan, R.,sekar, K.,Banerjee, R.,Sharma, V.,Surolia, A.,Vijayan, M.
      (1996) Nat.Struct.Mol.Biol. 3: 596


    Organizational Affiliation

    Molecular Biophysics Unit, UGC Centre of Advanced Study, Indian Institute of Science, Bangalore 560 012, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Agglutinin alpha chain
A
133Artocarpus integerMutation(s): 0 
Find proteins for P18670 (Artocarpus integer)
Go to UniProtKB:  P18670
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Agglutinin beta-3 chain
B
20Artocarpus integerMutation(s): 0 
Find proteins for P18673 (Artocarpus integer)
Go to UniProtKB:  P18673
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GAL
Query on GAL

Download SDF File 
Download CCD File 
A
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
MGC
Query on MGC

Download SDF File 
Download CCD File 
A
ALPHA-METHYL-N-ACETYL-D-GALACTOSAMINE
C9 H17 N O6
ZEVOCXOZYFLVKN-ZEBDFXRSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.189 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 43.287α = 90.00
b = 100.556β = 90.00
c = 102.399γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-09-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Data collection