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- PDB-5gtp: The agonist-free structure of human PPARgamma ligand binding doma... -
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Basic information
Entry | Database: PDB / ID: 5gtp | ||||||
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Title | The agonist-free structure of human PPARgamma ligand binding domain in the presence of the SRC-1 coactivator peptide | ||||||
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![]() | TRANSCRIPTION / PPARgamma / SRC-1 | ||||||
Function / homology | ![]() labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / 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 / positive regulation of transcription from RNA polymerase II promoter by galactose / MECP2 regulates transcription factors / positive regulation of female receptivity / negative regulation of extracellular matrix assembly ...labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / 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 / positive regulation of transcription from RNA polymerase II promoter by galactose / 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 / DNA binding domain binding / macrophage derived foam cell differentiation / positive regulation of vascular associated smooth muscle cell apoptotic process / STAT family protein binding / hypothalamus development / positive regulation of fatty acid metabolic process / male mating behavior / response to lipid / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / negative regulation of SMAD protein signal transduction / 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 / negative regulation of blood vessel endothelial cell migration / negative regulation of lipid storage / cellular response to low-density lipoprotein particle stimulus / negative regulation of BMP signaling pathway / white fat cell differentiation / cellular response to Thyroglobulin triiodothyronine / estrous cycle / 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 / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / BMP signaling pathway / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / long-chain fatty acid transport / nuclear retinoid X receptor binding / response to retinoic acid / histone acetyltransferase activity / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / cell maturation / negative regulation of signaling receptor activity / 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 / negative regulation of angiogenesis / cerebellum development / response to nutrient / BMAL1:CLOCK,NPAS2 activates circadian gene expression / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / negative regulation of MAP kinase activity / fatty acid metabolic process / Regulation of PTEN gene transcription / transcription coregulator binding / response to progesterone / hippocampus development / nuclear estrogen receptor binding / nuclear receptor binding / negative regulation of smooth muscle cell proliferation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptide binding / negative regulation of transforming growth factor beta receptor signaling pathway / Heme signaling / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / placenta development Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jang, J.Y. / Suh, S.W. | ||||||
![]() | ![]() Title: Structural basis for differential activities of enantiomeric PPAR gamma agonists: Binding of S35 to the alternate site. Authors: Jang, J.Y. / Koh, M. / Bae, H. / An, D.R. / Im, H.N. / Kim, H.S. / Yoon, J.Y. / Yoon, H.J. / Han, B.W. / Park, S.B. / Suh, S.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.3 KB | Display | ![]() |
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PDB format | ![]() | 51.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.9 KB | Display | ![]() |
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Full document | ![]() | 461.6 KB | Display | |
Data in XML | ![]() | 12.6 KB | Display | |
Data in CIF | ![]() | 16.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5gtnC ![]() 5gtoC ![]() 3vn2S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32280.350 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 223-505 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1905.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#3: Chemical | ChemComp-MYR / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.92 % |
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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 |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. obs: 16193 / % possible obs: 99.4 % / Redundancy: 5.8 % / Net I/σ(I): 36.2 |
Reflection shell | Resolution: 2.35→2.39 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 4 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3VN2 Resolution: 2.35→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 8.223 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.306 / ESU R Free: 0.238 / 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: 67.958 Å2
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Refinement step | Cycle: 1 / Resolution: 2.35→30 Å
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Refine LS restraints |
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