3WMH | pdb_00003wmh

Human PPAR gamma ligand binding domain in complex with a gammma selective synthetic partial agonist MEKT75

• PDB DOI: https://doi.org/10.2210/pdb3WMH/pdb

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


• Deposited: 2013-11-19 Released: 2014-11-19 
• Deposition Author(s): Oyama, T., Ohashi, M., Miyachi, H., Kusunoki, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.258 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Human PPRR gamma ligand binding domain in complex with a gammma selective synthetic partial agonist MEKT75

Oyama, T., Ohashi, M., Miyachi, H., Kusunoki, M.

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: 66.12 kDa 
• Atom Count: 4,313 
• Modeled Residue Count: 520 
• Deposited Residue Count: 572 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A, B	286	Homo sapiens	Mutation(s): 0  Gene Names: PPARG
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
JJA	C [auth A], D [auth B]	N-(phenylsulfonyl)-4-propoxy-3-({[4-(pyrimidin-2-yl)benzoyl]amino}methyl)benzamide C28 H26 N4 O5 S QEJZUENJDZMHGE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.258 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.249	α = 90
b = 61.113	β = 103.11
c = 119.28	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-19 
Deposition Author(s): Oyama, T., Ohashi, M., Miyachi, H., Kusunoki, M.

Revision History  

• Version 1.0: 2014-11-19
  Type: Initial release
  
• Version 1.1: 2016-03-02
  Changes: Structure summary
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description