8DK4 | pdb_00008dk4

Peroxisome proliferator-activated receptor gamma in complex with VSP-51-2

• PDB DOI: https://doi.org/10.2210/pdb8DK4/pdb

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


• Deposited: 2022-07-02 Released: 2023-07-05 
• Deposition Author(s): Ma, L., Zhou, X.E., Suino-Powell, K., Hou, N., Zhou, Z., Luo, J., Xu, H.E., Yi, W.
• Funding Organization(s): National Science Foundation (NSF, China)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.255 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.233 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

Identification of VSP-51-2 as the Novel and Safe PPAR gamma Modulator: Structure-Based Design, Biological Validation and Crystal Analysis

Ma, L., Zhou, X.E., Suino-Powell, K., Hou, N., Zhou, Z., Luo, J., Xu, H.E., Yi, W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 33.13 kDa 
• Atom Count: 2,281 
• Modeled Residue Count: 281 
• Deposited Residue Count: 287 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A	272	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma coactivator 1-alpha	B	15	Homo sapiens	Mutation(s): 0  Gene Names: PPARGC1A, LEM6, PGC1, PGC1A, PPARGC1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBK2 (Homo sapiens) Explore Q9UBK2  Go to UniProtKB:  Q9UBK2
PHAROS:  Q9UBK2 GTEx:  ENSG00000109819

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SJ9 (Subject of Investigation/LOI)	C [auth A]	5-(benzylcarbamoyl)-1-[(4-chloro-3-fluorophenyl)methyl]-1H-indole-2-carboxylic acid C24 H18 Cl F N2 O3 QNQATVBNODOSPT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.255 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.233 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.2	α = 90
b = 88.15	β = 90
c = 122.23	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-07-05 
Deposition Author(s): Ma, L., Zhou, X.E., Suino-Powell, K., Hou, N., Zhou, Z., Luo, J., Xu, H.E., Yi, W.

---

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	21877020
National Science Foundation (NSF, China)	China	22007020

Revision History  

• Version 1.0: 2023-07-05
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description