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Yorodumi- PDB-6ktn: Human PPARgamma ligand-binding domain R288A mutant in complex wit... -
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-Basic information
Entry | Database: PDB / ID: 6ktn | ||||||
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Title | Human PPARgamma ligand-binding domain R288A mutant in complex with imatinib | ||||||
Components |
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Keywords | TRANSCRIPTION / Type 2 diabetes mellitus | ||||||
Function / homology | Function and homology information labyrinthine layer morphogenesis / regulation of thyroid hormone mediated signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / 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 / MECP2 regulates transcription factors / positive regulation of female receptivity / negative regulation of extracellular matrix assembly ...labyrinthine layer morphogenesis / regulation of thyroid hormone mediated signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / 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 / MECP2 regulates transcription factors / positive regulation of female receptivity / negative regulation of extracellular matrix assembly / negative regulation of vascular endothelial cell proliferation / negative regulation of cellular response to transforming growth factor beta stimulus / 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 / macrophage derived foam cell differentiation / positive regulation of vascular associated smooth muscle cell apoptotic process / DNA binding domain binding / hypothalamus development / STAT family protein binding / male mating behavior / positive regulation of fatty acid metabolic process / response to lipid / negative regulation of SMAD protein signal transduction / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / LBD domain binding / negative regulation of type II interferon-mediated signaling pathway / negative regulation of cholesterol storage / E-box binding / alpha-actinin binding / lipid homeostasis / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / negative regulation of macrophage derived foam cell differentiation / cellular response to low-density lipoprotein particle stimulus / negative regulation of lipid storage / negative regulation of blood vessel endothelial cell migration / estrous cycle / negative regulation of BMP signaling pathway / cellular response to Thyroglobulin triiodothyronine / white fat cell differentiation / negative regulation of mitochondrial fission / Synthesis of bile acids and bile salts / positive regulation of cholesterol efflux / retinoic acid receptor signaling pathway / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / cell fate commitment / positive regulation of DNA binding / BMP signaling pathway / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / long-chain fatty acid transport / nuclear retinoid X receptor binding / response to retinoic acid / negative regulation of signaling receptor activity / histone acetyltransferase activity / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / cell maturation / histone acetyltransferase / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / epithelial cell differentiation / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / lactation / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / cerebellum development / negative regulation of angiogenesis / response to nutrient / BMAL1:CLOCK,NPAS2 activates circadian gene expression / fatty acid metabolic process / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / negative regulation of miRNA transcription / nuclear receptor coactivator activity / placenta development / response to progesterone / negative regulation of MAP kinase activity / Regulation of PTEN gene transcription / transcription coregulator binding / nuclear estrogen receptor binding / nuclear receptor binding / hippocampus development / negative regulation of smooth muscle cell proliferation / peptide binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / negative regulation of transforming growth factor beta receptor signaling pathway / Heme signaling / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.752 Å | ||||||
Authors | Jang, J.Y. / Han, B.W. | ||||||
Citation | Journal: Molecules / Year: 2019 Title: Structural Basis for the Regulation of PPAR gamma Activity by Imatinib. Authors: Jang, J.Y. / Kim, H.J. / Han, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ktn.cif.gz | 74.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ktn.ent.gz | 51.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ktn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kt/6ktn ftp://data.pdbj.org/pub/pdb/validation_reports/kt/6ktn | HTTPS FTP |
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-Related structure data
Related structure data | 6ktmC 6jq7S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32194.236 Da / Num. of mol.: 1 / Mutation: R316A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta2 / References: UniProt: P37231 |
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#2: Protein/peptide | Mass: 1905.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788, histone acetyltransferase |
#3: Chemical | ChemComp-STI / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.5 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.2 M sodium malonate (pH 7.0) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 26, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→50 Å / Num. obs: 10176 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 30.1 |
Reflection shell | Resolution: 2.75→2.8 Å / Rmerge(I) obs: 0.679 / Num. unique obs: 507 / % possible all: 99.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JQ7 Resolution: 2.752→30.002 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.893 / SU B: 11.654 / SU ML: 0.238 / Cross valid method: FREE R-VALUE / ESU R: 3.172 / ESU R Free: 0.362 Details: Hydrogens have been added in their 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: 44.711 Å2
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Refinement step | Cycle: LAST / Resolution: 2.752→30.002 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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