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Yorodumi- PDB-3et1: Structure of PPARalpha with 3-[5-Methoxy-1-(4-methoxy-benzenesulf... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3et1 | ||||||
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Title | Structure of PPARalpha with 3-[5-Methoxy-1-(4-methoxy-benzenesulfonyl)-1H-indol-3-yl]-propionic acid | ||||||
Components |
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Keywords | Transcription/Transferase / PPAR / PPARa / PPARalpha / Drug Discovery / Diabetes / adiponectin / metabolic disease / fragment-based drug discovery / scaffold-based drug discovery / Activator / DNA-binding / Metal-binding / Nucleus / Polymorphism / Receptor / Transcription / Transcription regulation / Zinc / Zinc-finger / Acyltransferase / Alternative splicing / Chromosomal rearrangement / Phosphoprotein / Proto-oncogene / Transferase / Ubl conjugation / Transcription-Transferase COMPLEX | ||||||
Function / homology | Function and homology information positive regulation of transformation of host cell by virus / regulation of fatty acid transport / regulation of fatty acid metabolic process / enamel mineralization / negative regulation of cell growth involved in cardiac muscle cell development / positive regulation of fatty acid oxidation / regulation of cellular ketone metabolic process / cellular response to fructose stimulus / behavioral response to nicotine / negative regulation of appetite ...positive regulation of transformation of host cell by virus / regulation of fatty acid transport / regulation of fatty acid metabolic process / enamel mineralization / negative regulation of cell growth involved in cardiac muscle cell development / positive regulation of fatty acid oxidation / regulation of cellular ketone metabolic process / cellular response to fructose stimulus / behavioral response to nicotine / negative regulation of appetite / positive regulation of fatty acid beta-oxidation / lipoprotein metabolic process / negative regulation of hepatocyte apoptotic process / mitogen-activated protein kinase kinase kinase binding / negative regulation of leukocyte cell-cell adhesion / labyrinthine layer morphogenesis / regulation of thyroid hormone mediated signaling pathway / ubiquitin conjugating enzyme binding / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / negative regulation of glycolytic process / negative regulation of sequestering of triglyceride / hypothalamus development / nuclear steroid receptor activity / male mating behavior / DNA-binding transcription activator activity / positive regulation of fatty acid metabolic process / nitric oxide metabolic process / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / positive regulation of ATP biosynthetic process / NFAT protein binding / negative regulation of cholesterol storage / estrous cycle / negative regulation of macrophage derived foam cell differentiation / cellular response to Thyroglobulin triiodothyronine / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Synthesis of bile acids and bile salts / negative regulation of cytokine production involved in inflammatory response / epidermis development / phosphatase binding / MDM2/MDM4 family protein binding / positive regulation of lipid biosynthetic process / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to retinoic acid / negative regulation of signaling receptor activity / negative regulation of reactive oxygen species biosynthetic process / histone acetyltransferase activity / Recycling of bile acids and salts / regulation of cellular response to insulin stimulus / positive regulation of gluconeogenesis / histone acetyltransferase / cellular response to hormone stimulus / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / positive regulation of neuron differentiation / RORA activates gene expression / cellular response to starvation / negative regulation of blood pressure / lactation / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / cerebellum development / response to nutrient / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / fatty acid metabolic process / nuclear receptor coactivator activity / Activation of gene expression by SREBF (SREBP) / negative regulation of miRNA transcription / response to progesterone / nuclear estrogen receptor binding / gluconeogenesis / nuclear receptor binding / hippocampus development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / response to insulin / SUMOylation of intracellular receptors / Heme signaling / mRNA transcription by RNA polymerase II / wound healing / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / transcription coactivator binding / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / male gonad development / nuclear receptor activity / Circadian Clock Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Zhang, K.Y.J. / Wang, W. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Scaffold-based discovery of indeglitazar, a PPAR pan-active anti-diabetic agent Authors: Artis, D.R. / Lin, J.J. / Zhang, C. / Wang, W. / Mehra, U. / Perreault, M. / Erbe, D. / Krupka, H.I. / England, B.P. / Arnold, J. / Plotnikov, A.N. / Marimuthu, A. / Nguyen, H. / Will, S. / ...Authors: Artis, D.R. / Lin, J.J. / Zhang, C. / Wang, W. / Mehra, U. / Perreault, M. / Erbe, D. / Krupka, H.I. / England, B.P. / Arnold, J. / Plotnikov, A.N. / Marimuthu, A. / Nguyen, H. / Will, S. / Signaevsky, M. / Kral, J. / Cantwell, J. / Settachatgull, C. / Yan, D.S. / Fong, D. / Oh, A. / Shi, S. / Womack, P. / Powell, B. / Habets, G. / West, B.L. / Zhang, K.Y. / Milburn, M.V. / Vlasuk, G.P. / Hirth, K.P. / Nolop, K. / Bollag, G. / Ibrahim, P.N. / Tobin, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3et1.cif.gz | 128.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3et1.ent.gz | 99.9 KB | Display | PDB format |
PDBx/mmJSON format | 3et1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/3et1 ftp://data.pdbj.org/pub/pdb/validation_reports/et/3et1 | HTTPS FTP |
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-Related structure data
Related structure data | 3et0C 3et2C 3et3C 1kkqS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 32874.246 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPARA, NR1C1, PPAR / Plasmid: pET-28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q07869 #2: Protein/peptide | Mass: 1965.281 Da / Num. of mol.: 2 / Fragment: residues 681-696 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NCOA1, SRC1 / Plasmid: pET-28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q15788, histone acetyltransferase #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.88 % |
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Crystal grow | Temperature: 277 K / pH: 8 Details: The purified PPARa LBD protein was diluted to 10 mg/ml and 1mM of indeglitazar and 2x molar excess of SRC-1 peptide were added prior to crystallization by mixing equal volumes of ...Details: The purified PPARa LBD protein was diluted to 10 mg/ml and 1mM of indeglitazar and 2x molar excess of SRC-1 peptide were added prior to crystallization by mixing equal volumes of protein/compound sample with reservoir solution containing 16% PEG 8000, 0.1 M Tris buffer at pH 8.0, 0.02 M lithium sulfate, and 5% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 14, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 26993 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rsym value: 0.045 |
Reflection shell | Resolution: 2.5→2.57 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 1.3 / Rsym value: 0.319 / % possible all: 99.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1KKQ Resolution: 2.5→44.8 Å / SU ML: 0.41 / σ(F): 1.35 / Phase error: 26.67 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.83 Å2 / ksol: 0.34 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.5→44.8 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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