1PXD

Crystal structure of the complex of jacalin with meso-tetrasulphonatophenylporphyrin.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Porphyrin binding to jacalin is facilitated by the inherent plasticity of the carbohydrate-binding site: novel mode of lectin-ligand interaction.

Goel, M.Anuradha, P.Kaur, K.J.Maiya, B.G.Swamy, M.J.Salunke, D.M.

(2004) Acta Crystallogr.,Sect.D 60: 281-288

  • DOI: 10.1107/S0907444903026684

  • PubMed Abstract: 
  • The crystal structure of the complex of meso-tetrasulfonatophenylporphyrin (H(2)TPPS) with jack fruit (Artocarpus integriflora) agglutinin (jacalin) has been determined at 1.8 A resolution. A porphyrin pair is sandwiched between two symmetry-related ...

    The crystal structure of the complex of meso-tetrasulfonatophenylporphyrin (H(2)TPPS) with jack fruit (Artocarpus integriflora) agglutinin (jacalin) has been determined at 1.8 A resolution. A porphyrin pair is sandwiched between two symmetry-related jacalin monomers in the crystal, leading to a cross-linking network of protein molecules. Apart from the stacking interactions, H(2)TPPS also forms hydrogen bonds, some involving water bridges, with jacalin at the carbohydrate-binding site. The residues that are involved in rendering galactopyranoside specificity to jacalin undergo conformational adjustments in order to accommodate the H(2)TPPS molecule. The water molecules at the carbohydrate-binding site of jacalin cement the jacalin-porphyrin interactions, optimizing their complementarity. Interactions of porphyrin with jacalin are relatively weak compared with those observed between galactopyranoside and jacalin, perhaps because the former largely involves water-mediated hydrogen bonds. While H(2)TPPS binds to jacalin at the carbohydrate-binding site as in the case of ConA, its mode of interaction with jacalin is very different. H(2)TPPS does not enter the carbohydrate-binding cavity of jacalin. Instead, it sits over the binding site. While the porphyrin binding is mediated by replicating the hydrogen-bonding network of mannopyranoside through the sulfonate atoms in the case of ConA, the plasticity associated with the carbohydrate-binding site accommodates the pluripotent porphyrin molecule in the case of jacalin through an entirely different set of interactions.


    Related Citations: 
    • Functional equality in the absence of structural similarity: an added dimension to molecular mimicry
      Goel, M.,Jain, D.,Kaur, K.J.,Kenoth, R.,Maiya, B.G.,Swamy, M.J.,Salunke, D.M.
      (2001) J.Biol.Chem. 276: 39277


    Organizational Affiliation

    National Institute of Immunology, New Delhi 110067, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Agglutinin alpha chain
A
133Artocarpus integerN/A
Find proteins for P18670 (Artocarpus integer)
Go to UniProtKB:  P18670
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Agglutinin beta-3 chain
B
20Artocarpus integerN/A
Find proteins for P18673 (Artocarpus integer)
Go to UniProtKB:  P18673
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SFP
Query on SFP

Download SDF File 
Download CCD File 
A
5,10,15,20-TETRAKIS(4-SULPFONATOPHENYL)-21H,23H-PORPHINE
C44 H34 N4 O12 S4
OVPFWIRROXFHGQ-LWQDQPMZSA-J
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SFPKa: 6500 M-1 BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.219 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 46.072α = 90.00
b = 101.890β = 90.00
c = 107.657γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MAR345data collection
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-02-03
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description