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- PDB-6kba: X-ray structure of human PPARalpha ligand binding domain-Wy14643 ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6kba | ||||||
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Title | X-ray structure of human PPARalpha ligand binding domain-Wy14643 co-crystals obtained by co-crystallization | ||||||
![]() | Peroxisome proliferator-activated receptor alpha | ||||||
![]() | TRANSCRIPTION / Nuclear receptor / Protein-ligand complex / PPAR | ||||||
Function / homology | ![]() 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 / ubiquitin conjugating enzyme binding / negative regulation of glycolytic process / negative regulation of sequestering of triglyceride / nuclear steroid receptor activity / DNA-binding transcription activator activity / nitric oxide metabolic process / positive regulation of fatty acid metabolic process / positive regulation of ATP biosynthetic process / NFAT protein binding / negative regulation of cholesterol storage / negative regulation of macrophage derived foam cell differentiation / negative regulation of cytokine production involved in inflammatory response / epidermis development / phosphatase binding / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of lipid biosynthetic process / negative regulation of reactive oxygen species biosynthetic process / negative regulation of signaling receptor activity / MDM2/MDM4 family protein binding / positive regulation of gluconeogenesis / RORA activates gene expression / negative regulation of blood pressure / Regulation of lipid metabolism by PPARalpha / cellular response to starvation / hormone-mediated signaling pathway / response to nutrient / BMAL1:CLOCK,NPAS2 activates circadian gene expression / negative regulation of miRNA transcription / Activation of gene expression by SREBF (SREBP) / fatty acid metabolic process / gluconeogenesis / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / wound healing / Heme signaling / SUMOylation of intracellular receptors / response to insulin / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / PPARA activates gene expression / Cytoprotection by HMOX1 / 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 / nuclear receptor activity / Circadian Clock / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / response to ethanol / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / cell differentiation / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / lipid binding / protein-containing complex binding / chromatin / 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 | ![]() ![]() ![]() ![]() | ||||||
![]() | Kamata, S. / Suda, K. / Saito, K. / Oyama, T. / Ishii, I. | ||||||
Funding support | ![]()
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![]() | ![]() Title: PPAR alpha Ligand-Binding Domain Structures with Endogenous Fatty Acids and Fibrates. Authors: Kamata, S. / Oyama, T. / Saito, K. / Honda, A. / Yamamoto, Y. / Suda, K. / Ishikawa, R. / Itoh, T. / Watanabe, Y. / Shibata, T. / Uchida, K. / Suematsu, M. / Ishii, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.2 KB | Display | ![]() |
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PDB format | ![]() | 50.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1000.4 KB | Display | ![]() |
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Full document | ![]() | 1004.1 KB | Display | |
Data in XML | ![]() | 12.9 KB | Display | |
Data in CIF | ![]() | 17.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6kaxC ![]() 6kayC ![]() 6kazC ![]() 6kb0C ![]() 6kb1C ![]() 6kb2C ![]() 6kb3C ![]() 6kb4C ![]() 6kb5C ![]() 6kb6C ![]() 6kb7C ![]() 6kb8C ![]() 6kb9C ![]() 6kypC ![]() 6l36C ![]() 6l37C ![]() 6l38C ![]() 6lx4C ![]() 6lx5C ![]() 6lx6C ![]() 6lx7C ![]() 6lx8C ![]() 6lx9C ![]() 6lxaC ![]() 6lxbC ![]() 6lxcC ![]() 7bpyC ![]() 7bpzC ![]() 7bq0C ![]() 7bq1C ![]() 7bq2C ![]() 7bq3C ![]() 7bq4C ![]() 3vi8S S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Components
#1: Protein | Mass: 30856.053 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.59 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / Details: 0.1 M HEPES (pH 7.0), 25 %(w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 16, 2019 / Details: Mirrors | |||||||||||||||||||||||||||
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: 1.82→43.22 Å / Num. obs: 25281 / % possible obs: 98.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 30.52 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.023 / Rpim(I) all: 0.015 / Rrim(I) all: 0.028 / Net I/σ(I): 24.3 / Num. measured all: 87369 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3VI8 Resolution: 1.82→26.733 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 28.82
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.8716 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.82→26.733 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.82→1.8572 Å / Rfactor Rfree error: 0
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