1LES

LENTIL LECTIN COMPLEXED WITH SUCROSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 3.0 of the entry. See complete history


Literature

NMR, molecular modeling, and crystallographic studies of lentil lectin-sucrose interaction.

Casset, F.Hamelryck, T.Loris, R.Brisson, J.R.Tellier, C.Dao-Thi, M.H.Wyns, L.Poortmans, F.Perez, S.Imberty, A.

(1995) J Biol Chem 270: 25619-25628

  • DOI: 10.1074/jbc.270.43.25619
  • Primary Citation of Related Structures:  
    1LES

  • PubMed Abstract: 
  • The conformational features of sucrose in the combining site of lentil lectin have been characterized through elucidation of a crystalline complex at 1.9-A resolution, transferred nuclear Overhauser effect experiments performed at 600 Mhz, and molecular modeling ...

    The conformational features of sucrose in the combining site of lentil lectin have been characterized through elucidation of a crystalline complex at 1.9-A resolution, transferred nuclear Overhauser effect experiments performed at 600 Mhz, and molecular modeling. In the crystal, the lentil lectin dimer binds one sucrose molecule per monomer. The locations of 229 water molecules have been identified. NMR experiments have provided 11 transferred NOEs. In parallel, the docking study and conformational analysis of sucrose in the combining site of lentil lectin indicate that three different conformations can be accommodated. Of these, the orientation with lowest energy is identical with the one observed in the crystalline complex and provides good agreement with the observed transferred NOEs. These structural investigations indicate that the bound sucrose has a unique conformation for the glycosidic linkage, close to the one observed in crystalline sucrose, whereas the fructofuranose ring remains relatively flexible and does not exhibit any strong interaction with the protein. Major differences in the hydrogen bonding network of sucrose are found. None of the two inter-residue hydrogen bonds in crystalline sucrose are conserved in the complex with the lectin. Instead, a water molecule bridges hydroxyl groups O2-g and O3-f of sucrose.


    Related Citations: 
    • Conserved Waters in Legume Lectin Crystal Structures: The Importance of Bound Waters for the Sequence-Structure Relationship within the Legume Lectin Family
      Loris, R., Stas, P.P.G., Wyns, L.
      (1994) J Mol Biol 269: 26722
    • Crystal Structure Determination and Refinement at 2.3 Angstroms Resolution of the Lentil Lectin
      Loris, R., Steyaert, J., Maes, D., Lisgarten, J., Pickersgill, R., Wyns, L.
      (1993) Biochemistry 32: 8772
    • Two Crystal Forms of the Lentil Lectin Diffract to High Resolution
      Loris, R., Lisgarten, J., Maes, D., Pickersgill, R., Koerber, F., Reynolds, C., Wyns, L.
      (1992) J Mol Biol 223: 579

    Organizational Affiliation

    Institut National de la Recherche Agronomique, Nantes, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LENTIL LECTIN AC181Lens culinarisMutation(s): 0 
Find proteins for P02870 (Lens culinaris)
Explore P02870 
Go to UniProtKB:  P02870
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
LENTIL LECTIN BD52Lens culinarisMutation(s): 0 
Find proteins for P02870 (Lens culinaris)
Explore P02870 
Go to UniProtKB:  P02870
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
G, H
2 N/A Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download Ideal Coordinates CCD File 
A, C
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
A, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900003
Query on PRD_900003
G, HsucroseOligosaccharide /  Nutrient

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.03α = 90
b = 124.8β = 111.8
c = 50.02γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
MADNESdata reduction
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-12-07
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other
  • Version 1.4: 2018-04-18
    Changes: Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 3.0: 2020-10-14
    Changes: Atomic model, Data collection, Derived calculations, Structure summary