1LEN

REFINEMENT OF TWO CRYSTAL FORMS OF LENTIL LECTIN AT 1.8 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural analysis of two crystal forms of lentil lectin at 1.8 A resolution.

Loris, R.Van Overberge, D.Dao-Thi, M.H.Poortmans, F.Maene, N.Wyns, L.

(1994) Proteins 20: 330-346

  • DOI: 10.1002/prot.340200406
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structures of two crystal forms of lentil lectin are determined and refined at high resolution. Orthorhombic lentil lectin is refined at 1.80 A resolution to an R-factor of 0.184 and monoclinic lentil lectin at 1.75 A resolution to an R-factor of ...

    The structures of two crystal forms of lentil lectin are determined and refined at high resolution. Orthorhombic lentil lectin is refined at 1.80 A resolution to an R-factor of 0.184 and monoclinic lentil lectin at 1.75 A resolution to an R-factor of 0.175. These two structures are compared to each other and to the other available legume lectin structures. The monosaccharide binding pocket of each lectin monomer contains a tightly bound phosphate ion. This phosphate makes hydrogen bonding contacts with Asp-81 beta, Gly-99 beta, and Asn-125 beta, three residues that are highly conserved in most of the known legume lectin sequences and essential for monosaccharide recognition in all legume lectin crystal structures described thus far. A detailed analysis of the composition and properties of the hydrophobic contact network and hydrophobic nuclei in lentil lectin is presented. Contact map calculations reveal that dense clusters of nonpolar as well as polar side chains play a major role in secondary structure packing. This is illustrated by a large cluster of 24 mainly hydrophobic amino acids that is responsible for the majority of packing interactions between the two beta-sheets. Another series of four smaller and less hydrophobic clusters is found to mediate the packing of a number of loop structures upon the front sheet. A very dense, but not very conserved cluster is found to stabilize the transition metal binding site. The highly conserved and invariant nonpolar residues are distributed asymmetrically over the protein.


    Related Citations: 
    • 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 Difract to High Resolution
      Loris, R.,Lisgarten, J.,Maes, D.,Pickersgill, R.,Korber, F.,Reynolds, C.,Wyns, L.
      (1992) J.Mol.Biol. 223: 579


    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, C
181Lens culinarisMutation(s): 0 
Find proteins for P02870 (Lens culinaris)
Go to UniProtKB:  P02870
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LECTIN
B, D
52Lens culinarisMutation(s): 0 
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, C
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, C
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 58.490α = 90.00
b = 56.370β = 104.40
c = 82.730γ = 90.00
Software Package:
Software NamePurpose
RESTRAINrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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