5EZP

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.210 

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

  • 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; Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transthyretin
A, B, C, D, E, F, G, H
122Homo sapiensGene Names: TTR (PALB)
Find proteins for P02766 (Homo sapiens)
Go to Gene View: TTR
Go to UniProtKB:  P02766
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
G
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
IPJ
Query on IPJ

Download SDF File 
Download CCD File 
A, B, C, F, G
4-hydroxy-chalcone
C15 H12 O2
PWWCDTYUYPOAIU-DHZHZOJOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.210 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 62.480α = 90.00
b = 62.480β = 90.00
c = 238.320γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
Cootmodel building
XDSdata reduction
REFMACrefinement
MxCuBEdata collection
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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