1KGJ

Rat transthyretin (also called prealbumin) complex with 3',5'-dibromoflavone (EMD21388)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Comparison of binding interactions of dibromoflavonoids with transthyretin.

Muziol, T.Cody, V.Wojtczak, A.

(2001) Acta Biochim.Pol. 48: 885-892


  • PubMed Abstract: 
  • The crystal structure of rat transthyretin (rTTR) complex with the dibromoflavone EMD21388 was determined to 2.3 A resolution and refined to R = 0.203 and Rfree = 0.288. Two different orientations of EMD21388, which differ in the channel penetration ...

    The crystal structure of rat transthyretin (rTTR) complex with the dibromoflavone EMD21388 was determined to 2.3 A resolution and refined to R = 0.203 and Rfree = 0.288. Two different orientations of EMD21388, which differ in the channel penetration by 1.6 A, were found in the A/C binding site of rTTR. The single ligand position observed in the BID site is intermediate between the two positions found in the A/C site. The position of the dibromoflavone in the B/D site is similar to that reported for dibromoaurone in human TTR. The bromine atoms of EMD21388 form strong interactions in the P3 and P3' pockets of rTTR. Due to the different molecular architectures of both ligands, dibromoflavone forms only one interaction with Lys-15 near the channel entrance, while direct interactions with the pair of Lys-15 were reported for dibromoaurone. The C3* methyl group of EMD21388 mediates the bridging interactions between two TTR subunits in the P2 pockets. The interactions of the O2* hydroxyl group of dibromoaurone with the Thr-119 side chain in the P3 pockets are not matched by similar interactions in EMD21388. Both these alternative interactions can explain the competitive binding of 3',5'-dibromoflavonoids to transthyretin.


    Related Citations: 
    • 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.,Sect.D 52: 758
    • 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.,Sect.D 57: 1061
    • 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.,Sect.D 57: 957
    • 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
    • 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


    Organizational Affiliation

    Institute of Chemistry, Nicolaus Copernicus University, ToruĊ„, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRANSTHYRETIN
A, B, C, D
127Rattus norvegicusGene Names: Ttr (Tt)
Find proteins for P02767 (Rattus norvegicus)
Go to UniProtKB:  P02767
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FL8
Query on FL8

Download SDF File 
Download CCD File 
B, C
6,4'-DIHYDROXY-3-METHYL-3',5'-DIBROMOFLAVONE
C16 H10 Br2 O4
GKDYOXMZSXVKPP-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.203 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 82.545α = 90.00
b = 82.545β = 90.00
c = 161.741γ = 90.00
Software Package:
Software NamePurpose
R-AXISdata scaling
R-AXISdata reduction
CNSrefinement
R-AXISdata collection
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-11-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance