+Open data
-Basic information
Entry | Database: PDB / ID: 1y0s | ||||||
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Title | Crystal structure of PPAR delta complexed with GW2331 | ||||||
Components | Peroxisome proliferator activated receptor delta | ||||||
Keywords | HORMONE/GROWTH FACTOR RECEPTOR / PPAR / HORMONE-GROWTH FACTOR RECEPTOR COMPLEX | ||||||
Function / homology | Function and homology information fat cell proliferation / positive regulation of fat cell proliferation / keratinocyte migration / linoleic acid binding / positive regulation of skeletal muscle tissue regeneration / axon ensheathment / regulation of skeletal muscle satellite cell proliferation / glucose transmembrane transport / positive regulation of myoblast proliferation / fatty acid catabolic process ...fat cell proliferation / positive regulation of fat cell proliferation / keratinocyte migration / linoleic acid binding / positive regulation of skeletal muscle tissue regeneration / axon ensheathment / regulation of skeletal muscle satellite cell proliferation / glucose transmembrane transport / positive regulation of myoblast proliferation / fatty acid catabolic process / positive regulation of fatty acid metabolic process / negative regulation of cholesterol storage / Carnitine metabolism / negative regulation of myoblast differentiation / Signaling by Retinoic Acid / nuclear steroid receptor activity / positive regulation of fat cell differentiation / cell-substrate adhesion / fatty acid beta-oxidation / decidualization / keratinocyte proliferation / fatty acid transport / generation of precursor metabolites and energy / cellular response to nutrient levels / hormone-mediated signaling pathway / adipose tissue development / energy homeostasis / negative regulation of miRNA transcription / fatty acid metabolic process / embryo implantation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cholesterol metabolic process / lipid metabolic process / apoptotic signaling pathway / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / wound healing / Nuclear Receptor transcription pathway / transcription coactivator binding / nuclear receptor activity / glucose metabolic process / negative regulation of epithelial cell proliferation / sequence-specific double-stranded DNA binding / cellular response to hypoxia / DNA-binding transcription factor binding / cell population proliferation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / lipid binding / regulation of transcription by RNA polymerase II / positive regulation of gene expression / positive regulation of DNA-templated transcription / chromatin / apoptotic process / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Takada, I. / Yu, R.T. / Xu, H.E. / Xu, R.X. / Lambert, M.H. / Montana, V.G. / Kliewer, S.A. / Evans, R.M. / Umesono, K. | ||||||
Citation | Journal: MOL.ENDOCRINOL. / Year: 2000 Title: Alteration of a Single Amino Acid in Peroxisome Proliferator-Activated Receptor-alpha (PPARalpha) Generates a PPAR delta Phenotype Authors: Takada, I. / Yu, R.T. / Xu, H.E. / Lambert, M.H. / Montana, V.G. / Kliewer, S.A. / Evans, R.M. / Umesono, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y0s.cif.gz | 122.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y0s.ent.gz | 95.1 KB | Display | PDB format |
PDBx/mmJSON format | 1y0s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1y0s_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 1y0s_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 1y0s_validation.xml.gz | 25.6 KB | Display | |
Data in CIF | 1y0s_validation.cif.gz | 34.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y0/1y0s ftp://data.pdbj.org/pub/pdb/validation_reports/y0/1y0s | HTTPS FTP |
-Related structure data
Related structure data | 2gwxS 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: 31114.178 Da / Num. of mol.: 2 / Fragment: LBD domain (residues 170-441) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): B21 / References: UniProt: Q03181 #2: Chemical | ChemComp-IOD / #3: Chemical | #4: Sugar | #5: 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: 1.5 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 Details: PEG 35K, KI, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 180 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 7, 1997 |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→50 Å / Num. all: 20426 / Num. obs: 19351 / % possible obs: 94.7 % / Observed criterion σ(F): 2.6 / Observed criterion σ(I): 2.6 / Redundancy: 4 % / Biso Wilson estimate: 37.6 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.65→2.74 Å / Redundancy: 4 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1963 / Rsym value: 0.413 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2GWX Resolution: 2.65→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.65→50 Å
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Refine LS restraints |
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