5EZP

Human transthyretin (TTR) complexed with 4-hydroxy-chalcone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A new crystal form of human transthyretin obtained with a curcumin derived ligand.

Polsinelli, I.Nencetti, S.Shepard, W.Ciccone, L.Orlandini, E.Stura, E.A.

(2016) J Struct Biol 194: 8-17

  • DOI: 10.1016/j.jsb.2016.01.007
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Transthyretin (TTR), a 54kDa homotetrameric protein that transports thyroxine (T4), has been associated with clinical cases of TTR amyloidosis for its tendency to aggregate to form fibrils. Many ligands with a potential to inhibit fibril formation ha ...

    Transthyretin (TTR), a 54kDa homotetrameric protein that transports thyroxine (T4), has been associated with clinical cases of TTR amyloidosis for its tendency to aggregate to form fibrils. Many ligands with a potential to inhibit fibril formation have been studied by X-ray crystallography in complex with TTR. Unfortunately, the ligand is often found in ambiguous electron density that is difficult to interpret. The ligand validation statistics suggest over-interpretation, even for the most active compounds like diflunisal. The primary technical reason is its position on a crystallographic 2-fold axis in the most common crystal form. Further investigations with the use of polyethylene glycol (PEG) to crystallize TTR complexes have resulted in a new trigonal polymorph with two tetramers in the asymmetric unit. The ligand used to obtain this new polymorph, 4-hydroxychalcone, is related to curcumin. Here we evaluate this crystal form to understand the contribution it may bring to the study of TTR ligands complexes, which are often asymmetric.


    Organizational Affiliation

    Synchrotron SOLEIL, l'Orme des Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette, France; CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), Gif-sur-Yvette F-91191, France. Electronic address: estura@cea.fr.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transthyretin
A, B, C, D, E, F, G, H
122Homo sapiensMutation(s): 0 
Gene Names: TTRPALB
Find proteins for P02766 (Homo sapiens)
Go to UniProtKB:  P02766
NIH Common Fund Data Resources
PHAROS  P02766
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IPJ
Query on IPJ

Download CCD File 
A, B, C, F, G
4-hydroxy-chalcone
C15 H12 O2
PWWCDTYUYPOAIU-DHZHZOJOSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
G
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.48α = 90
b = 62.48β = 90
c = 238.32γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2016-02-10
    Changes: Database references
  • Version 1.2: 2016-03-02
    Changes: Database references