3WJ5 | pdb_00003wj5

Crystal structure of PPARgamma ligand binding domain in complex with triphenyltin

• PDB DOI: https://doi.org/10.2210/pdb3WJ5/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-10-04 Released: 2014-10-15 
• Deposition Author(s): Harada, S., Hiromori, Y., Fukakusa, S., Kawahara, K., Nakamura, S., Noda, M., Uchiyama, S., Fukui, K., Nishikawa, J., Nagase, H., Kobayashi, Y., Ohkubo, T., Yoshida, T., Nakanishi, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.247 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Literature

Structural basis for PPARgamma transactivation by endocrine disrupting organotin compounds

Harada, S., Hiromori, Y., Fukakusa, S., Kawahara, K., Nakamura, S., Noda, M., Uchiyama, S., Fukui, K., Nishikawa, J., Nagase, H., Kobayashi, Y., Ohkubo, T., Yoshida, T., Nakanishi, T.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 63.52 kDa 
• Atom Count: 4,419 
• Modeled Residue Count: 516 
• Deposited Residue Count: 552 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A, B	276	Homo sapiens	Mutation(s): 0  Gene Names: PPARG, NR1C3
UniProt & NIH Common Fund Data Resources
Find proteins for P37231 (Homo sapiens) Explore P37231  Go to UniProtKB:  P37231
PHAROS:  P37231 GTEx:  ENSG00000132170

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
T9T	C [auth A], D [auth B]	triphenylstannanyl C18 H15 Sn NFHRNKANAAGQOH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free:  0.247 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.521	α = 90
b = 88.492	β = 91.06
c = 57.943	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-15 
Deposition Author(s): Harada, S., Hiromori, Y., Fukakusa, S., Kawahara, K., Nakamura, S., Noda, M., Uchiyama, S., Fukui, K., Nishikawa, J., Nagase, H., Kobayashi, Y., Ohkubo, T., Yoshida, T., Nakanishi, T.

Revision History  

• Version 1.0: 2014-10-15
  Type: Initial release
  
• Version 2.0: 2019-06-12
  Changes: Atomic model, Data collection
• Version 2.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations