4R6O

Jacalin-carbohydrate interactions. Distortion of the ligand as a determinant of affinity.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Jacalin-carbohydrate interactions: distortion of the ligand molecule as a determinant of affinity.

Abhinav, K.V.Sharma, K.Swaminathan, C.P.Surolia, A.Vijayan, M.

(2015) Acta Crystallogr D Biol Crystallogr 71: 324-331

  • DOI: 10.1107/S139900471402553X
  • Primary Citation of Related Structures:  
    4R6N, 4R6O, 4R6P, 4R6Q, 4R6R

  • PubMed Abstract: 
  • Jacalin is among the most thoroughly studied lectins. Its carbohydrate-binding site has also been well characterized. It has been postulated that the lower affinity of β-galactosides for jacalin compared with α-galactosides is caused by steric interactions of the substituents in the former with the protein ...

    Jacalin is among the most thoroughly studied lectins. Its carbohydrate-binding site has also been well characterized. It has been postulated that the lower affinity of β-galactosides for jacalin compared with α-galactosides is caused by steric interactions of the substituents in the former with the protein. This issue has been explored energetically and structurally using different appropriate carbohydrate complexes of jacalin. It turns out that the earlier postulation is not correct. The interactions of the substituent with the binding site remain essentially the same irrespective of the anomeric nature of the substitution. This is achieved through a distortion of the sugar ring in β-galactosides. The difference in energy, and therefore in affinity, is caused by a distortion of the sugar ring in β-galactosides. The elucidation of this unprecedented distortion of the ligand as a strategy for modulating affinity is of general interest. The crystal structures also provide a rationale for the relative affinities of the different carbohydrate ligands for jacalin.


    Related Citations: 
    • 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 Biol 3: 596
    • Crystal structure of the jacalin-T-antigen complex and a comparative study of lectin-T-antigen complexes.
      Jeyaprakash, A.A., Geetha Rani, P., Banuprakash Reddy, G., Banumathi, S., Betzel, C., Sekar, K., Surolia, A., Vijayan, M.
      (2002) J Mol Biol 321: 637
    • 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
    • Structural basis for the energetics of jacalin-sugar interactions: promiscuity versus specificity.
      Arockia Jeyaprakash, A., Jayashree, G., Mahanta, S.K., Swaminathan, C.P., Sekar, K., Surolia, A., Vijayan, M.
      (2005) J Mol Biol 347: 181
    • Structural basis for the unusual carbohydrate-binding specificity of jacalin towards galactose and mannose.
      Bourne, Y., Astoul, C.H., Zamboni, V., Peumans, W.J., Menu-Bouaouiche, L., Van Damme, E.J., Barre, A., Rouge, P.
      (2002) Biochem J 364: 173

    Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Agglutinin alpha chainA, C, E, G133Artocarpus integerMutation(s): 0 
UniProt
Find proteins for P18670 (Artocarpus integer)
Explore P18670 
Go to UniProtKB:  P18670
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18670
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Agglutinin beta-3 chainB, D, F, H19Artocarpus integerMutation(s): 0 
UniProt
Find proteins for P18673 (Artocarpus integer)
Explore P18673 
Go to UniProtKB:  P18673
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18673
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLA
Query on GLA

Download Ideal Coordinates CCD File 
J [auth A],
M [auth C],
O [auth E],
Y [auth G]
alpha-D-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PHYPRBDBSA-N
 Ligand Interaction
ZZ1
Query on ZZ1

Download Ideal Coordinates CCD File 
I [auth A],
L [auth C],
N [auth E],
X [auth G]
4-METHYL-2H-CHROMEN-2-ONE
C10 H8 O2
PSGQCCSGKGJLRL-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
P [auth E],
Q [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
IPA
Query on IPA

Download Ideal Coordinates CCD File 
AA [auth G],
BA [auth G],
CA [auth G],
K [auth A],
R [auth E],
AA [auth G],
BA [auth G],
CA [auth G],
K [auth A],
R [auth E],
S [auth E],
T [auth E],
U [auth E],
V [auth F],
W [auth F],
Z [auth G]
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.59α = 90
b = 82.18β = 106.76
c = 63.31γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-18
    Type: Initial release
  • Version 1.1: 2015-02-25
    Changes: Database references
  • Version 1.2: 2019-12-04
    Changes: Data collection, Derived calculations
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary