1FAT

PHYTOHEMAGGLUTININ-L


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The crystallographic structure of phytohemagglutinin-L.

Hamelryck, T.W.Dao-Thi, M.H.Poortmans, F.Chrispeels, M.J.Wyns, L.Loris, R.

(1996) J Biol Chem 271: 20479-20485

  • DOI: 10.1074/jbc.271.34.20479
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The structure of phytohemagglutinin-L (PHA-L), a leucoagglutinating seed lectin from Phaseolus vulgaris, has been solved with molecular replacement using the coordinates of lentil lectin as model, and refined at a resolution of 2.8 A. The final R-fac ...

    The structure of phytohemagglutinin-L (PHA-L), a leucoagglutinating seed lectin from Phaseolus vulgaris, has been solved with molecular replacement using the coordinates of lentil lectin as model, and refined at a resolution of 2.8 A. The final R-factor of the structure is 20.0%. The quaternary structure of the PHA-L tetramer differs from the structures of the concanavalin A and peanut lectin tetramers, but resembles the structure of the soybean agglutinin tetramer. PHA-L consists of two canonical legume lectin dimers that pack together through the formation of a close contact between two beta-strands. Of the two covalently bound oligosaccharides per monomer, only one GlcNAc residue per monomer is visible in the electron density. In this article we describe the structure of PHA-L, and we discuss the putative position of the high affinity adenine-binding site present in a number of legume lectins. A comparison with transthyretin, a protein that shows a remarkable resemblance to PHA-L, gives further ground to our proposal.


    Related Citations: 
    • Crystallization of Glycosylated and Nonglycosylated Phytohemagglutinin-L
      Dao-Thi, M.H., Hamelryck, T.W., Poortmans, F., Voelker, T.A., Chrispeels, M.J., Wyns, L.
      (1996) Proteins 24: 134
    • Lectins, Lectin Genes, and Their Role in Plant Defense
      Chrispeels, M.J., Raikhel, N.V.
      (1991) Plant Cell 3: 1
    • Characterization of Two Phaseolus Vulgaris Phytohemagglutinin Genes Closely Linked on the Chromosome
      Hoffman, L.M., Donaldson, D.D.
      (1985) EMBO J 4: 883

    Organizational Affiliation

    Dienst Ultrastructuur, Vlaams Interuniversitair Instituut voor Biotechnologie, Vrije Universiteit Brussel, Paardenstraat 65, B-1640 Sint-Genesius-Rode, Belgium.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHYTOHEMAGGLUTININ-L
A, B, C, D
252Phaseolus vulgarisMutation(s): 0 
Gene Names: DLEC2
Find proteins for P05087 (Phaseolus vulgaris)
Go to UniProtKB:  P05087
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MN
Query on MN

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.3α = 90
b = 121.2β = 93.7
c = 90.8γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
MADNESdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-12-23
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance