3B0Q

Human PPAR gamma ligand binding domain in complex with MCC555

• PDB DOI: https://doi.org/10.2210/pdb3B0Q/pdb

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


• Deposited: 2011-06-13 Released: 2011-08-10 
• Deposition Author(s): Tomioka, D., Hashimoto, H., Sato, M., Shimizu, T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.229 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 

Starting Model: experimental

Literature

Crystal structure of human PPAR gamma in complex with MCC555

Tomioka, D., Hashimoto, H., Sato, M., Shimizu, 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: 62.95 kDa 
• Atom Count: 4,220 
• Modelled Residue Count: 507 
• Deposited Residue Count: 548 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A, B	274	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
MC5	C [auth A]	(5S)-5-({6-[(2-fluorobenzyl)oxy]naphthalen-2-yl}methyl)-1,3-thiazolidine-2,4-dione C21 H16 F N O3 S PKWDZWYVIHVNKS-IBGZPJMESA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
MC5	BindingDB:  3B0Q	EC50: 3.00e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.229 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.252	α = 90
b = 59.812	β = 103.89
c = 117.846	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-10 
Deposition Author(s): Tomioka, D., Hashimoto, H., Sato, M., Shimizu, T.

Revision History  

• Version 1.0: 2011-08-10
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description