6D8X | pdb_00006d8x

PPAR gamma LBD complexed with the agonist GW1929

PDB DOI: https://doi.org/10.2210/pdb6D8X/pdb

Classification: dna binding protein/AGONIST
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-04-27 Released: 2019-05-01
Deposition Author(s): Mou, T.C., Chrisman, I.M., Hughes, T.S., Sprang, S.R.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.245 (Depositor), 0.241 (DCC)
R-Value Work:
0.205 (Depositor), 0.205 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

PPAR gamma LBD complexed with the agonist GW1929

Chrisman, I.M., Mou, T.C., Sprang, S.R., Hughes, T.S.

To be published.

Macromolecule Content

Total Structure Weight: 35 kDa
Atom Count: 2,460
Modeled Residue Count: 276
Deposited Residue Count: 297
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A	297	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P37231
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDK Query on EDK Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(2~{S})-3-[4-[2-[methyl(pyridin-2-yl)amino]ethoxy]phenyl]-2-[[2-(phenylcarbonyl)phenyl]amino]propanoic acid C₃₀ H₂₉ N₃ O₄ QTQMRBZOBKYXCG-MHZLTWQESA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
EDK	BindingDB: 6D8X	Ki: min: 0.05, max: 104 (nM) from 6 assay(s)
EDK	BindingDB: 6D8X	EC50: min: 1.5, max: 389 (nM) from 16 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.245 (Depositor), 0.241 (DCC)
R-Value Work: 0.205 (Depositor), 0.205 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.934	α = 90
b = 61.934	β = 90
c = 167.92	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-05-01

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P20GM103546
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	R00DK103116

Revision History (Full details and data files)

Version 1.0: 2019-05-01
Type: Initial release
Version 1.1: 2019-12-25
Changes: Author supporting evidence
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description