1LEM

THE MONOSACCHARIDE BINDING SITE OF LENTIL LECTIN: AN X-RAY AND MOLECULAR MODELLING STUDY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The monosaccharide binding site of lentil lectin: an X-ray and molecular modelling study.

Loris, R.Casset, F.Bouckaert, J.Pletinckx, J.Dao-Thi, M.H.Poortmans, F.Imberty, A.Perez, S.Wyns, L.

(1994) Glycoconj.J. 11: 507-517


  • PubMed Abstract: 
  • The X-ray crystal structure of lentil lectin in complex with alpha-D-glucopyranose has been determined by molecular replacement and refined to an R-value of 0.20 at 3.0 A resolution. The glucose interacts with the protein in a manner similar to that ...

    The X-ray crystal structure of lentil lectin in complex with alpha-D-glucopyranose has been determined by molecular replacement and refined to an R-value of 0.20 at 3.0 A resolution. The glucose interacts with the protein in a manner similar to that found in the mannose complexes of concanavalin A, pea lectin and isolectin I from Lathyrus ochrus. The complex is stabilized by a network of hydrogen bonds involving the carbohydrate oxygens O6, O4, O3 and O5. In addition, the alpha-D-glucopyranose residue makes van der Waals contacts with the protein, involving the phenyl ring of Phe123 beta. The overall structure of lentil lectin, at this resolution, does not differ significantly from the highly refined structures of the uncomplexed lectin. Molecular docking studies were performed with mannose and its 2-O and 3-O-m-nitro-benzyl derivatives to explain their high affinity binding. The interactions of the modelled mannose with lentil lectin agree well with those observed experimentally for the protein-carbohydrate complex. The highly flexible Me-2-O-(m-nitro-benzyl)-alpha-D-mannopyranoside and Me-3-O-(m-nitro-benzyl)-alpha-D-mannopyranoside become conformationally restricted upon binding to lentil lectin. For best orientations of the two substrates in the combining site, the loss of entropy is accompanied by the formation of a strong hydrogen bond between the nitro group and one amino acid, Gly97 beta and Asn125 beta, respectively, along with the establishment of van der Waals interactions between the benzyl group and the aromatic amino acids Tyr100 beta and Trp128 beta.


    Related Citations: 
    • Two Crystal Forms of the Lentil Lectin Diffract to High Resolution
      Loris, R.,Lisgarten, J.,Maes, D.,Pickersgill, R.,Korber, 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

    Laboratorium voor Ultrastructuur, Vrije Universiteit Brussel, Sint-Genesius-Rode, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LECTIN
A
181Lens culinarisN/A
Find proteins for P02870 (Lens culinaris)
Go to UniProtKB:  P02870
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LECTIN
B
52Lens culinarisN/A
Find proteins for P02870 (Lens culinaris)
Go to UniProtKB:  P02870
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Work: 0.206 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 85.710α = 90.00
b = 85.710β = 90.00
c = 165.380γ = 120.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1993-11-17 
  • Released Date: 1994-01-31 
  • Deposition Author(s): Loris, R., Wyns, L.

Revision History 

  • Version 1.0: 1994-01-31
    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