Crystal Structure of Pokeweed Lectin-D2

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 

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This is version 1.3 of the entry. See complete history


Structures of two lectins from the roots of pokeweed (Phytolacca americana).

Fujii, T.Hayashida, M.Hamasu, M.Ishiguro, M.Hata, Y.

(2004) Acta Crystallogr D Biol Crystallogr 60: 665-673

  • DOI: https://doi.org/10.1107/S090744490400232X
  • Primary Citation of Related Structures:  
    1UHA, 1ULN

  • PubMed Abstract: 

    Pokeweed lectin (PL), a lectin specific for N-acetylglucosamine-containing saccharides, stimulates peripheral lymphocytes to undergo mitosis by binding to their cell surfaces. Four types of lectins have been isolated from the roots of pokeweed (Phytolacca americana) and shown to contain homologous domains but to have different molecular sizes and biological properties. PL-D, the smallest lectin in the group, has two isolectins, PL-D1 and PL-D2. PL-D1 consists of 84 amino-acid residues, while PL-D2 is identical to PL-D1 in sequence except for the lack of two C-terminal residues, Leu83 and Thr84. The crystal structures of PL-D1 and PL-D2 were solved by the molecular-replacement method and refined to 1.65 and 1.5 A resolution with R factors of 17.2 and 17.6%, respectively. The PL-Ds are composed of two repetitive chitin-binding domains, each of which has four S-S bridges and one putative carbohydrate-binding site. The two carbohydrate-binding sites in PL-D are located on one side of the molecule. The relative orientation of the two domains in PL-D1 differs from that in PL-D2. Two C-terminal residues of PL-D1 are invisible in the present crystal structure, indicating the flexibility of the region. PL-D2 has a Ca2+ ion bound to the C-terminus on the molecular surface. A wide distribution of acidic residues is characteristically observed on one side of the C-terminal region of PL-D.

  • Organizational Affiliation

    Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
lectin-D282Phytolacca americanaMutation(s): 0 
Find proteins for P83790 (Phytolacca americana)
Explore P83790 
Go to UniProtKB:  P83790
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP83790
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CA

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 23.24α = 90
b = 56.95β = 109.3
c = 29.62γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-04-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations