1ZGS

Parkia platycephala seed lectin in complex with 5-bromo-4-chloro-3-indolyl-a-D-mannose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The first crystal structure of a mimosoideae lectin reveals a novel quaternary arrangement of a widespread domain.

Gallego Del Sol, F.Nagano, C.Cavada, B.S.Calvete, J.J.

(2005) J.Mol.Biol. 353: 574-583

  • DOI: 10.1016/j.jmb.2005.08.055
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystal structures of the apo and mannose-bound Parkia platycephala seed lectin represent the first structure of a Mimosoideae lectin and a novel circular arrangement of beta-prism domains, and highlight the adaptability of the beta-prism fold as ...

    The crystal structures of the apo and mannose-bound Parkia platycephala seed lectin represent the first structure of a Mimosoideae lectin and a novel circular arrangement of beta-prism domains, and highlight the adaptability of the beta-prism fold as a building block in the evolution of plant lectins. The P.platycephala lectin is a dimer both in solution and in the crystals. Mannose binding to each of the three homologous carbohydrate-recognition domains of the lectin occurs through different modes, and restrains the flexibility of surface-exposed loops and residues involved in carbohydrate recognition. The planar array of carbohydrate-binding sites on the rim of the toroid-shaped structure of the P.platycephala lectin dimer immediately suggests a mechanism to promote multivalent interactions leading to cross-linking of carbohydrate ligands as part of the host strategy against phytopredators and pathogens. The cyclic structure of the P.platycephala lectin points to the convergent evolution of a structural principle for the construction of lectins involved in host defense or in attacking other organisms.


    Organizational Affiliation

    Instituto de Biomedicina de Valencia, CSIC, E-46010 Valencia, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mannose/glucose-specific lectin
A, B
447Parkia platycephalaMutation(s): 0 
Find proteins for P83304 (Parkia platycephala)
Go to UniProtKB:  P83304
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XMM
Query on XMM

Download SDF File 
Download CCD File 
A, B
(2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL
(5-BROMO-4-CHLORO-3-INDOLYL)-A-D-MANNOSE
C14 H15 Br Cl N O6
OPIFSICVWOWJMJ-HAAGFXOZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 80.239α = 90.00
b = 114.177β = 119.88
c = 80.304γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SOLVEphasing
REFMACrefinement
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-10-11
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance