1JN2

Crystal Structure of meso-tetrasulphonatophenyl porphyrin complexed with Concanavalin A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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.

(2000) J.Biol.Chem. 276: 39277-39281

  • DOI: 10.1074/jbc.M105387200

  • PubMed Abstract: 
  • The crystal structure of meso-tetrasulfonatophenylporphyrin complexed with concanavalin A (ConA) was determined at 1.9 A resolution. Comparison of this structure with that of ConA bound to methyl alpha-d-mannopyranoside provided direct structural evi ...

    The crystal structure of meso-tetrasulfonatophenylporphyrin complexed with concanavalin A (ConA) was determined at 1.9 A resolution. Comparison of this structure with that of ConA bound to methyl alpha-d-mannopyranoside provided direct structural evidence of molecular mimicry in the context of ligand receptor binding. The sulfonatophenyl group of meso-tetrasulfonatophenylporphyrin occupies the same binding site on ConA as that of methyl alpha-d-mannopyranoside, a natural ligand. A pair of stacked porphyrin molecules stabilizes the crystal structure by end-to-end cross-linking with ConA resulting in a network similar to that observed upon agglutination of cells by lectins. The porphyrin binds to ConA predominantly through hydrogen bonds and water-mediated interactions. The sandwiched water molecules in the complex play a cementing role, facilitating favorable binding of porphyrin. Seven of the eight hydrogen bonds observed between methyl alpha-d-mannopyranoside and ConA are mimicked by the sulfonatophenyl group of porphyrin after incorporating two water molecules. Thus, the similarity in chemical interactions was manifested in terms of functional mimicry despite the obvious structural dissimilarity between the sugar and the porphyrin.


    Organizational Affiliation

    Structural Biology Unit, National Institute of Immunology, New Delhi 110067, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Concanavalin-A
P
237Canavalia ensiformisN/A
Find proteins for P02866 (Canavalia ensiformis)
Go to UniProtKB:  P02866
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
P
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
SFP
Query on SFP

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Download CCD File 
P
5,10,15,20-TETRAKIS(4-SULPFONATOPHENYL)-21H,23H-PORPHINE
C44 H34 N4 O12 S4
OVPFWIRROXFHGQ-LWQDQPMZSA-J
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
P
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SFPKa: 12200 M-1 BINDINGMOAD
SFPKd: 82000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.195 
  • Space Group: F 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 106.000α = 90.00
b = 117.300β = 90.00
c = 126.000γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
AMoREphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-07-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-06-28
    Type: Database references, Source and taxonomy, Structure summary