1KGI | pdb_00001kgi

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

• PDB DOI: https://doi.org/10.2210/pdb1KGI/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Rattus norvegicus
• Mutation(s): No 


• Deposited: 2001-11-27 Released: 2002-11-27 
• Deposition Author(s): Wojtczak, A., Neumann, P., Muziol, T., Cody, V., Luft, J.R., Pangborn, W.

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Experimental Data Snapshot

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

Starting Model: experimental

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

• PubMed: 11995998 
• Primary Citation 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 8-1.8 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.

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Organizational Affiliation: 
• Institute of Chemistry, Nicolaus Copernicus University, Toruń, Poland.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 55.95 kDa 
• Atom Count: 4,106 
• Modeled Residue Count: 481 
• Deposited Residue Count: 508 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRANSTHYRETIN	A, B, C, D	127	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P02767 (Rattus norvegicus) Explore P02767  Go to UniProtKB:  P02767

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
T4A	E [auth C], F [auth D]	3,3',5,5'-TETRAIODOTHYROACETIC ACID C14 H8 I4 O4 PPJYSSNKSXAVDB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.51	α = 90
b = 81.51	β = 90
c = 160.238	γ = 90

Software Package:

Software Name	Purpose
HAMLIN/UCSD	data collection
HAMLIN/UCSD	data reduction
CNS	refinement
UCSD-system	data reduction
UCSD-system	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-11-27 
Deposition Author(s): Wojtczak, A., Neumann, P., Muziol, T., Cody, V., Luft, J.R., Pangborn, W.

Revision History  

• 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
• Version 1.4: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description