1KGI

Rat transthyretin (also called prealbumin) complex with 3,3',5,5'-tetraiodothyroacetic acid (t4ac)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Complex of rat transthyretin with tetraiodothyroacetic acid refined at 2.1 and 1.8 A resolution.

Muziol, T.Cody, V.Luft, J.R.Pangborn, W.Wojtczak, A.

(2001) Acta Biochim Pol 48: 877-884

  • Primary Citation of Related Structures:  
    1KGI

  • PubMed Abstract: 
  • The crystal structure of rat transthyretin (rTTR) complex with 3,5,3',5'-tetraiodothyroacetic acid (T4Ac) was determined at 1.8 A resolution with low temperature synchrotron data collected at CHESS. The structure was refined to R = 0.207 and Rfree = 0.24 with the use of 8-1 ...

    The crystal structure of rat transthyretin (rTTR) complex with 3,5,3',5'-tetraiodothyroacetic acid (T4Ac) was determined at 1.8 A resolution with low temperature synchrotron data collected at CHESS. The structure was refined to R = 0.207 and Rfree = 0.24 with the use of 8-1.8 A data. The additional 8000 reflections from the incomplete 2.1-1.8 data shell, included in the refinement, reduced the Rfree index by 1.3%. Structure comparison with the model refined against the complete 8-2.1 A data revealed no differences in the ligand orientation and the conformation of the polypeptide chain in the core regions. However, the high-resolution data included in the refinement improved the model in the flexible regions poorly defined with the lower resolution data. Also additional sixteen water molecules were found in the difference map calculated with the extended data. The structure revealed both forward and reverse binding of tetraiodothyroacetic acid in one binding site and two modes of forward ligand binding in the second site, with the phenolic iodine atoms occupying different sets of the halogen binding pockets.


    Related Citations: 
    • Structural Aspects of Inotropic Bipyridine Binding. Crystal Structure Determination to 1.9 A of the Human Serum Transthyretin-Milrinone Complex
      Wojtczak, A., Luft, J.R., Cody, V.
      (1993) J Biol Chem 268: 6202
    • Mechanism of Molecular Recognition. Structural Aspects of 3,3'-Diiodo-L-Thyronine Binding to Human Serum Transthyretin
      Wojtczak, A., Luft, J., Cody, V.
      (1992) J Biol Chem 267: 353
    • Structures of Human Transthyretin Complexed with Thyroxine at 2.0 A Resolution and 3',5'-Dinitro-N-Acetyl-L-Thyronine at 2.2 A Resolution
      Wojtczak, A., Cody, V., Luft, J.R., Pangborn, W.
      (1996) Acta Crystallogr D Biol Crystallogr 52: 758
    • Structure of New Polymorphic Monoclinic Form of Hum Transthyretin at 3A Resolution Reveals a Mixed Comp between Unliganded and T4-Bound Tetramers of Ttr
      Wojtczak, A., Neumann, P., Cody, V.
      (2001) Acta Crystallogr D Biol Crystallogr 57: 957
    • STRUCTURE OF RAT (rTTR) TRANSTHYRETIN COMPLEX WITH THYROXINE AT 2.5 A RESOLUTION: FIRST NON-BIASED INS INTO THYROXINE BINDING REVEALS DIFFERENT HORMONE ORIENTATION IN TWO BINDING SITES
      Wojtczak, A., Cody, V., Luft, J., Pangborn, W.
      (2001) Acta Crystallogr D Biol Crystallogr 57: 1061

    Organizational Affiliation

    Institute of Chemistry, Nicolaus Copernicus University, Toruń, Poland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRANSTHYRETINA, B, C, D127Rattus norvegicusMutation(s): 0 
Gene Names: TtrTt
UniProt
Find proteins for P02767 (Rattus norvegicus)
Explore P02767 
Go to UniProtKB:  P02767
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02767
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
T4A
Query on T4A

Download Ideal Coordinates CCD File 
E [auth C],
F [auth D]
3,3',5,5'-TETRAIODOTHYROACETIC ACID
C14 H8 I4 O4
PPJYSSNKSXAVDB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.204 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.51α = 90
b = 81.51β = 90
c = 160.238γ = 90
Software Package:
Software NamePurpose
HAMLIN/UCSDdata collection
HAMLIN/UCSDdata reduction
CNSrefinement
UCSD-systemdata reduction
UCSD-systemdata scaling
CNSphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-11-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-04-04
    Changes: Data collection, Refinement description