6TDC | pdb_00006tdc

PPAR gamma ligand binding domain in complex with MRL-871

PDB DOI: https://doi.org/10.2210/pdb6TDC/pdb

Classification: GENE REGULATION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-11-08 Released: 2020-11-18
Deposition Author(s): de Vries, R.M.J.M., Leijten-van de Gevel, I.A., van Herk, K.H.N., Brunsveld, L.
Funding Organization(s): Netherlands Organisation for Scientific Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free:
0.239 (Depositor), 0.244 (DCC)
R-Value Work:
0.201 (Depositor), 0.214 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Binding of PPAR(gamma) to MRL871

Leijten-van de Gevel, I.A., van Herk, K.H.N., de Vries, R.M.J.M., Brunsveld, L.

To be published.

Macromolecule Content

Total Structure Weight: 33.84 kDa
Atom Count: 2,155
Modeled Residue Count: 260
Deposited Residue Count: 292
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A	292	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4F1 (Subject of Investigation/LOI) Query on 4F1 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]	4-{1-[2-chloro-6-(trifluoromethyl)benzoyl]-1H-indazol-3-yl}benzoic acid C₂₂ H₁₂ Cl F₃ N₂ O₃ DANLZOIRUUHIIX-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free: 0.239 (Depositor), 0.244 (DCC)
R-Value Work: 0.201 (Depositor), 0.214 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.142	α = 90
b = 93.142	β = 90
c = 130.574	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
Aimless	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: 2020-11-18

Deposition Author(s):

de Vries, R.M.J.M.

Leijten-van de Gevel, I.A.

van Herk, K.H.N.

Funding Organization	Location	Grant Number
Netherlands Organisation for Scientific Research	Netherlands	024.001.035

Revision History (Full details and data files)

Version 1.0: 2020-11-18
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.