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- PDB-5u3y: Human PPARdelta ligand-binding domain in complexed with specific ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5u3y | |||||||||
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Title | Human PPARdelta ligand-binding domain in complexed with specific agonist 9 | |||||||||
![]() | Peroxisome proliferator-activated receptor delta | |||||||||
![]() | protein binding/activator / PPARdelta / ligand-binding domain / agonist / protein binding-activator complex | |||||||||
Function / homology | ![]() 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 / Carnitine metabolism / negative regulation of myoblast differentiation / Signaling by Retinoic Acid / nuclear steroid receptor activity / positive regulation of fatty acid metabolic process / cell-substrate adhesion / fatty acid beta-oxidation / negative regulation of cholesterol storage / decidualization / keratinocyte proliferation / fatty acid transport / positive regulation of fat cell differentiation / cellular response to nutrient levels / adipose tissue development / energy homeostasis / embryo implantation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / hormone-mediated signaling pathway / cholesterol metabolic process / negative regulation of miRNA transcription / fatty acid metabolic process / generation of precursor metabolites and energy / apoptotic signaling pathway / wound healing / lipid metabolic process / transcription coactivator binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / Nuclear Receptor transcription pathway / glucose metabolic process / negative regulation of epithelial cell proliferation / nuclear receptor activity / 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 / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / apoptotic process / positive regulation of DNA-templated transcription / 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 | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wu, C.-C. / Baiga, T.J. / Downes, M. / La Clair, J.J. / Atkins, A.R. / Richard, S.B. / Stockley-Noel, T.A. / Bowman, M.E. / Evans, R.M. / Noel, J.P. | |||||||||
![]() | ![]() Title: Structural basis for specific ligation of the peroxisome proliferator-activated receptor delta. Authors: Wu, C.C. / Baiga, T.J. / Downes, M. / La Clair, J.J. / Atkins, A.R. / Richard, S.B. / Fan, W. / Stockley-Noel, T.A. / Bowman, M.E. / Noel, J.P. / Evans, R.M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 325.4 KB | Display | ![]() |
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PDB format | ![]() | 271.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5u3qC ![]() 5u3rC ![]() 5u3sC ![]() 5u3tC ![]() 5u3uC ![]() 5u3vC ![]() 5u3wC ![]() 5u3xC ![]() 5u3zC ![]() 5u40C ![]() 5u41C ![]() 5u42C ![]() 5u43C ![]() 5u44C ![]() 5u45C ![]() 5u46C ![]() 1gwzS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein / Sugars , 2 types, 4 molecules AB![](data/chem/img/B7G.gif)
![](data/chem/img/B7G.gif)
#1: Protein | Mass: 31114.178 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Ligand-binding domain / Source: (gene. exp.) ![]() ![]() ![]() #2: Sugar | |
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-Non-polymers , 4 types, 117 molecules ![](data/chem/img/7U7.gif)
![](data/chem/img/PGO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PGO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PEG / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57.05 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Bis-tris propane, potassium chloride, PEG 8000, 1,2-propandiol, EDTA, DTT PH range: 7.5 - 8.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→95.18 Å / Num. obs: 54673 / % possible obs: 91.5 % / Redundancy: 3.4 % / CC1/2: 0.986 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 1.85→1.89 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 0.7 / CC1/2: 0.395 / % possible all: 70.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1GWZ Resolution: 1.9→95.182 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.36 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→95.182 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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