1LES

LENTIL LECTIN COMPLEXED WITH SUCROSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.4 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

  • 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 molecu ...

    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
    • 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
    • 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


    Organizational Affiliation

    Institut National de la Recherche Agronomique, Nantes, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LENTIL LECTIN
A, C
181Lens culinarisMutation(s): 0 
Find proteins for P02870 (Lens culinaris)
Go to UniProtKB:  P02870
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LENTIL LECTIN
B, D
52Lens culinarisMutation(s): 0 
Find proteins for P02870 (Lens culinaris)
Go to UniProtKB:  P02870
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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

Download SDF File 
Download CCD File 
A, C
FRUCTOSE
C6 H12 O6
RFSUNEUAIZKAJO-ARQDHWQXSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
GLC
Query on GLC

Download SDF File 
Download CCD File 
A, C
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 50.030α = 90.00
b = 124.800β = 111.80
c = 50.020γ = 90.00
Software Package:
Software NamePurpose
MADNESdata reduction
X-PLORrefinement
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-12-07
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other
  • Version 1.4: 2018-04-18
    Type: Data collection