3KMG | pdb_00003kmg

The X-ray Crystal Structure of PPAR-gamma in Complex with an Indole Derivative Modulator, GSK538, and an SRC-1 Peptide

PDB DOI: https://doi.org/10.2210/pdb3KMG/pdb

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

Deposited: 2009-11-10 Released: 2010-01-12
Deposition Author(s): Gampe, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.230 (Depositor), 0.231 (DCC)
R-Value Work:
0.198 (Depositor), 0.199 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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Literature

Synthesis and biological activities of novel indole derivatives as potent and selective PPAR-gamma modulators

Lamotte, Y., Martres, P., Faucher, N., Laroze, A., Grillot, D., Ancellin, N., Saintillan, Y., Beneton, V., Gampe, R.

To be published.

Macromolecule Content

Total Structure Weight: 68.88 kDa
Atom Count: 4,569
Modeled Residue Count: 544
Deposited Residue Count: 598
Unique protein chains: 2

Macromolecules

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

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Steroid Receptor Coactivator-1	B, D [auth E]	27	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
538 Query on 538 Download:Ideal Coordinates CCD File SDF format, chain F [auth D] SDF format, chain E [auth A] MOL2 format, chain F [auth D] MOL2 format, chain E [auth A] mmCIF format, chain F [auth D] mmCIF format, chain E [auth A]	E [auth A], F [auth D]	4'-[(2,3-dimethyl-5-{[(1S)-1-phenylpropyl]carbamoyl}-1H-indol-1-yl)methyl]biphenyl-2-carboxylic acid C₃₄ H₃₂ N₂ O₃ GAGNYMUXGIUCTR-HKBQPEDESA-N		Interactions Focus chain E [auth A] Focus chain F [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.230 (Depositor), 0.231 (DCC)
R-Value Work: 0.198 (Depositor), 0.199 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.335	α = 90
b = 84.158	β = 90
c = 96.425	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
JDirector	data collection
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-01-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-01-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2018-01-24
Changes: Database references
Version 1.4: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2024-03-13
Changes: Source and taxonomy, Structure summary
Version 1.6: 2024-10-30
Changes: Structure summary

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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.