2B14

The crystal structure of 2,4-dinitrophenol in complex with the amyloidogenic variant Transthyretin Leu 55 Pro


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The binding of 2,4-dinitrophenol to wild-type and amyloidogenic transthyretin

Morais-de-Sa, E.Neto-Silva, R.M.Pereira, P.J.Saraiva, M.J.Damas, A.M.

(2006) ACTA CRYSTALLOGR.,SECT.D 62: 512-519

  • DOI: 10.1107/S0907444906006962
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Systemic deposition of transthyretin (TTR) amyloid fibrils is always observed in familial amyloidotic polyneuropathy, senile systemic amyloidosis and familial amyloidotic cardiomyopathy patients. Destabilization of the molecule leads to a cascade of ...

    Systemic deposition of transthyretin (TTR) amyloid fibrils is always observed in familial amyloidotic polyneuropathy, senile systemic amyloidosis and familial amyloidotic cardiomyopathy patients. Destabilization of the molecule leads to a cascade of events which result in fibril formation. The destabilization of a native protein with consequent conformational changes appears to be a common link in several human amyloid diseases. Intensive research has been directed towards finding small molecules that could work as therapeutic agents for the prevention/inhibition of amyloid diseases through stabilization of the native fold of the potentially amyloidogenic protein. This work provides insight into the structural determinants of the highly stabilizing effects of 2,4-dinitrophenol on wild-type TTR. It is also shown that similar interactions are established between this molecule and two highly amyloidogenic TTR variants: TTR L55P and TTR Y78F. In the three crystal complexes, 2,4-dinitrophenol occupies the two hormone-binding sites of the TTR tetramer. As a result of 2,4-dinitrophenol binding, the two dimers in the TTR tetramer become closer, increasing the stability of the protein. The three-dimensional structures now determined allow a comprehensive description of key interactions between transthyretin and 2,4-dinitrophenol, a small compound that holds promise as a template for the design of a therapeutical drug for amyloid diseases.


    Organizational Affiliation

    Instituto de Biologia Molecular e Celular-IBMC, Rua do Campo Alegre 823, 4150-180 Porto, Portugal.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transthyretin
A, B
127Homo sapiensMutations: L55P
Gene Names: TTR (PALB)
Find proteins for P02766 (Homo sapiens)
Go to Gene View: TTR
Go to UniProtKB:  P02766
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DNF
Query on DNF

Download SDF File 
Download CCD File 
A, B
2,4-DINITROPHENOL
C6 H4 N2 O5
UFBJCMHMOXMLKC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.203 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 42.550α = 90.00
b = 84.247β = 90.00
c = 63.397γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
CCP4data scaling
ARP/wARPmodel building
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-07-18
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance