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Yorodumi- PDB-6k0t: Crystal Structure of PPARgamma Ligand Binding Domain in complex w... -
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-Basic information
Entry | Database: PDB / ID: 6k0t | ||||||
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Title | Crystal Structure of PPARgamma Ligand Binding Domain in complex with dibenzooxepine derivative compound-17 | ||||||
Components |
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Keywords | NUCLEAR PROTEIN / PPARgamma / Ligand binding domain / PPARg modulator / Cancer | ||||||
Function / homology | Function and homology information positive regulation of mitochondrial DNA metabolic process / positive regulation of muscle tissue development / positive regulation of cellular respiration / positive regulation of fatty acid oxidation / : / : / lncRNA binding / cellular respiration / prostaglandin receptor activity / regulation of cholesterol transporter activity ...positive regulation of mitochondrial DNA metabolic process / positive regulation of muscle tissue development / positive regulation of cellular respiration / positive regulation of fatty acid oxidation / : / : / lncRNA binding / cellular respiration / prostaglandin receptor activity / regulation of cholesterol transporter activity / negative regulation of connective tissue replacement involved in inflammatory response wound healing / negative regulation of receptor signaling pathway via STAT / response to muscle activity / MECP2 regulates transcription factors / negative regulation of extracellular matrix assembly / negative regulation of vascular endothelial cell proliferation / negative regulation of cellular response to transforming growth factor beta stimulus / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / negative regulation of cardiac muscle hypertrophy in response to stress / arachidonic acid binding / positive regulation of low-density lipoprotein receptor activity / positive regulation of adiponectin secretion / lipoprotein transport / negative regulation of sequestering of triglyceride / temperature homeostasis / positive regulation of vascular associated smooth muscle cell apoptotic process / macrophage derived foam cell differentiation / DNA binding domain binding / STAT family protein binding / positive regulation of fatty acid metabolic process / response to lipid / negative regulation of SMAD protein signal transduction / response to starvation / positive regulation of ATP biosynthetic process / LBD domain binding / negative regulation of type II interferon-mediated signaling pathway / negative regulation of cholesterol storage / response to dietary excess / E-box binding / alpha-actinin binding / negative regulation of blood vessel endothelial cell migration / lipid homeostasis / intracellular glucose homeostasis / fatty acid oxidation / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / positive regulation of cholesterol efflux / negative regulation of macrophage derived foam cell differentiation / cellular response to low-density lipoprotein particle stimulus / negative regulation of lipid storage / negative regulation of BMP signaling pathway / white fat cell differentiation / negative regulation of mitochondrial fission / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / long-chain fatty acid transport / retinoic acid receptor signaling pathway / positive regulation of DNA binding / cell fate commitment / BMP signaling pathway / adipose tissue development / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / nuclear retinoid X receptor binding / energy homeostasis / brown fat cell differentiation / negative regulation of signaling receptor activity / regulation of cellular response to insulin stimulus / cell maturation / positive regulation of gluconeogenesis / digestion / positive regulation of adipose tissue development / epithelial cell differentiation / respiratory electron transport chain / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / mitochondrion organization / negative regulation of angiogenesis / response to nutrient / negative regulation of MAP kinase activity / RNA splicing / SUMOylation of transcription cofactors / fatty acid metabolic process / nuclear receptor coactivator activity / negative regulation of miRNA transcription / placenta development / Regulation of PTEN gene transcription / negative regulation of smooth muscle cell proliferation / gluconeogenesis / transcription coregulator binding / nuclear receptor binding / transcription initiation at RNA polymerase II promoter / transcription coregulator activity / peptide binding / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / SUMOylation of intracellular receptors / Heme signaling / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||
Authors | Suzuki, M. / Yamamoto, K. / Takahashi, Y. / Saito, J. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2019 Title: Development of a novel class of peroxisome proliferator-activated receptor (PPAR) gamma ligands as an anticancer agent with a unique binding mode based on a non-thiazolidinedione scaffold. Authors: Yamamoto, K. / Tamura, T. / Nakamura, R. / Hosoe, S. / Matsubara, M. / Nagata, K. / Kodaira, H. / Uemori, T. / Takahashi, Y. / Suzuki, M. / Saito, J.I. / Ueno, K. / Shuto, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k0t.cif.gz | 247.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k0t.ent.gz | 207 KB | Display | PDB format |
PDBx/mmJSON format | 6k0t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k0/6k0t ftp://data.pdbj.org/pub/pdb/validation_reports/k0/6k0t | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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: 32769.941 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Production host: Escherichia coli (E. coli) / References: UniProt: P37231 #2: Protein/peptide | Mass: 1355.662 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UBK2*PLUS #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: 2.4 Å3/Da / Density % sol: 48.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.05M Magnesium acetate, 0.1M Sodium acetate, 12% PEG 8,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 13, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→43.96 Å / Num. obs: 52839 / % possible obs: 95.8 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 1.84→1.94 Å / Redundancy: 2 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 7640 / % possible all: 95 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→40 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / SU B: 9.2 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.146 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.27 Å2
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Refinement step | Cycle: 1 / Resolution: 1.84→40 Å
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