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Yorodumi- PDB-2npa: the crystal structure of the human PPARaplpha ligand binding doma... -
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-Basic information
Entry | Database: PDB / ID: 2npa | ||||||
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Title | the crystal structure of the human PPARaplpha ligand binding domain in complex with a a-hydroxyimino phenylpropanoic acid | ||||||
Components |
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Keywords | TRANSCRIPTION / protein-agonist complex | ||||||
Function / homology | Function and homology information positive regulation of transformation of host cell by virus / regulation of fatty acid transport / enamel mineralization / regulation of fatty acid metabolic process / negative regulation of cell growth involved in cardiac muscle cell development / positive regulation of fatty acid oxidation / cellular response to fructose stimulus / regulation of cellular ketone metabolic process / behavioral response to nicotine / negative regulation of appetite ...positive regulation of transformation of host cell by virus / regulation of fatty acid transport / enamel mineralization / regulation of fatty acid metabolic process / negative regulation of cell growth involved in cardiac muscle cell development / positive regulation of fatty acid oxidation / cellular response to fructose stimulus / regulation of cellular ketone metabolic process / 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 / ubiquitin conjugating enzyme binding / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / negative regulation of glycolytic process / positive regulation of female receptivity / negative regulation of sequestering of triglyceride / nuclear steroid receptor activity / DNA-binding transcription activator activity / hypothalamus development / nitric oxide metabolic process / positive regulation of fatty acid metabolic process / male mating behavior / positive regulation of ATP biosynthetic process / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / NFAT protein binding / negative regulation of cholesterol storage / negative regulation of macrophage derived foam cell differentiation / cellular response to Thyroglobulin triiodothyronine / estrous cycle / Synthesis of bile acids and bile salts / negative regulation of cytokine production involved in inflammatory response / epidermis development / phosphatase binding / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / positive regulation of lipid biosynthetic process / nuclear retinoid X receptor binding / negative regulation of reactive oxygen species biosynthetic process / response to retinoic acid / histone acetyltransferase activity / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / negative regulation of signaling receptor activity / histone acetyltransferase / MDM2/MDM4 family protein binding / cellular response to hormone stimulus / positive regulation of gluconeogenesis / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / negative regulation of blood pressure / lactation / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / cellular response to starvation / hormone-mediated signaling pathway / 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 / fatty acid metabolic process / gluconeogenesis / response to progesterone / hippocampus development / nuclear estrogen receptor binding / nuclear receptor binding / 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 / wound healing / Heme signaling / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / response to insulin / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / transcription coactivator binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / male gonad development / Circadian Clock Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Kim, K.H. / Chung, H.K. / Han, H.O. / Kim, S.H. / Koh, J.S. / Kim, G.T. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2007 Title: Design and synthesis of oxime ethers of alpha-acyl-beta-phenylpropanoic acids as PPAR dual agonists Authors: Han, H.O. / Kim, S.H. / Kim, K.H. / Hur, G.C. / Yim, H.J. / Chung, H.K. / Woo, S.H. / Koo, K.D. / Lee, C.S. / Koh, J.S. / Kim, G.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2npa.cif.gz | 120.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2npa.ent.gz | 93.1 KB | Display | PDB format |
PDBx/mmJSON format | 2npa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2npa_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 2npa_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2npa_validation.xml.gz | 28.3 KB | Display | |
Data in CIF | 2npa_validation.cif.gz | 39.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/2npa ftp://data.pdbj.org/pub/pdb/validation_reports/np/2npa | HTTPS FTP |
-Related structure data
Related structure data | 1k7lS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30513.596 Da / Num. of mol.: 2 / Fragment: ligand binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q07869 #2: Protein/peptide | Mass: 1848.177 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: chemically synthesized 21 mer portion of the human SRC-1 References: UniProt: Q2T9G5, UniProt: Q15788*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: 2.79 Å3/Da / Density % sol: 55.98 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: 6% PEG 10K. 0.1M Hepes, 6% ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.54 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Feb 20, 2004 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→20 Å / Num. all: 31665 / Num. obs: 29916 / % possible obs: 95.9 % / Rmerge(I) obs: 0.059 / Χ2: 1.434 / Net I/σ(I): 18.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1K7L Resolution: 2.3→20 Å / σ(F): 0
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Solvent computation | Bsol: 52.306 Å2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.979 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Xplor file |
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