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Yorodumi- PDB-7vwe: Human peroxisome proliferator-activated receptor (PPAR) delta lig... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vwe | ||||||
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Title | Human peroxisome proliferator-activated receptor (PPAR) delta ligand binding domain in complex with a synthetic partial agonist JK122 | ||||||
Components | Peroxisome proliferator-activated receptor delta | ||||||
Keywords | TRANSCRIPTION / NUCLEAR RECEPTOR / PROTEIN-LIGAND COMPLEX / PPAR | ||||||
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 / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Oyama, T. / Miyachi, H. | ||||||
Funding support | 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2022 Title: Crystal structures of the ligand-binding domain of human peroxisome proliferator-activated receptor delta in complexes with phenylpropanoic acid derivatives and a pyridine carboxylic acid derivative. Authors: Oyama, T. / Takiguchi, K. / Miyachi, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vwe.cif.gz | 143.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vwe.ent.gz | 90.9 KB | Display | PDB format |
PDBx/mmJSON format | 7vwe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vw/7vwe ftp://data.pdbj.org/pub/pdb/validation_reports/vw/7vwe | HTTPS FTP |
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-Related structure data
Related structure data | 7vwfC 7vwgC 7vwhC 2znpS 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: 31527.648 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPARD, NR1C2, PPARB / Production host: Escherichia coli (E. coli) / References: UniProt: Q03181 #2: Sugar | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.72 Å3/Da / Density % sol: 54.85 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 22% Polyethyleneglycol, 200 mM potassium thiocyanate, 0.5% N-HEPTYL-BETA-D-GLUCOPYRANOSIDE |
-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: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 11, 2013 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 26118 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 57.18 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.06 / Rrim(I) all: 0.117 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 3→3.18 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.48 / Num. unique obs: 2163 / CC1/2: 0.932 / Rpim(I) all: 0.287 / Rrim(I) all: 0.561 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2znp Resolution: 3→47.57 Å / SU ML: 0.4532 / Cross valid method: FREE R-VALUE / σ(F): 0.2 / Phase error: 24.7644 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.67 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→47.57 Å
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Refine LS restraints |
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LS refinement shell |
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