4R6R

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

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Ligand Structure Quality Assessment 


This is version 2.1 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: https://doi.org/10.1107/S139900471402553X
  • Primary Citation of Related Structures:  
    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. 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.


  • 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
MoleculeChains Sequence LengthOrganismDetailsImage
Agglutinin alpha chain
A, C, E, G
133Artocarpus 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
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Agglutinin beta-3 chain
B, D, F, H
19Artocarpus 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
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
147
Query on 147

Download Ideal Coordinates CCD File 
I [auth A],
U [auth E],
V [auth G]
4-nitrophenyl beta-D-galactopyranoside
C12 H15 N O8
IFBHRQDFSNCLOZ-YBXAARCKSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
J [auth A]
K [auth A]
L [auth A]
M [auth A]
N [auth A]
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
P [auth C],
Q [auth C],
R [auth C],
S [auth C],
T [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
IPA
Query on IPA

Download Ideal Coordinates CCD File 
O [auth A]ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
147 Binding MOAD:  4R6R Ka: 2370 (M^-1) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.44α = 90
b = 80.25β = 107.68
c = 62.97γ = 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
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary