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Yorodumi- PDB-3ho0: Crystal structure of the PPARgamma-LBD complexed with a new arylo... -
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-Basic information
Entry | Database: PDB / ID: 3ho0 | ||||||
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Title | Crystal structure of the PPARgamma-LBD complexed with a new aryloxy-3phenylpropanoic acid | ||||||
Components | Peroxisome proliferator-activated receptor gamma | ||||||
Keywords | TRANSCRIPTION / BUNDLE OF ALPHA-HELICES / SMALL FOUR-STRANDED BETA-SHEET / Activator / Alternative splicing / Diabetes mellitus / Disease mutation / DNA-binding / Metal-binding / Nucleus / Obesity / Phosphoprotein / Polymorphism / Receptor / Transcription regulation / Zinc / Zinc-finger | ||||||
Function / homology | Function and homology information Complex I biogenesis / Respiratory electron transport / mitochondrial ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / : / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / Mitochondrial protein degradation / NADH dehydrogenase (ubiquinone) activity / mitochondrial membrane ...Complex I biogenesis / Respiratory electron transport / mitochondrial ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / : / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / Mitochondrial protein degradation / NADH dehydrogenase (ubiquinone) activity / mitochondrial membrane / aerobic respiration / mitochondrial inner membrane / mitochondrion / nucleoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Pochetti, G. / Montanari, R. / Mazza, F. / Loiodice, F. / Fracchiolla, G. / Laghezza, A. / Lavecchia, A. / Novellino, E. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2009 Title: New 2-Aryloxy-3-phenyl-propanoic Acids As Peroxisome Proliferator-Activated Receptors alpha/gamma Dual Agonists with Improved Potency and Reduced Adverse Effects on Skeletal Muscle Function Authors: Fracchiolla, G. / Laghezza, A. / Piemontese, L. / Tortorella, P. / Mazza, F. / Montanari, R. / Pochetti, G. / Lavecchia, A. / Novellino, E. / Pierno, S. / Conte Camerino, D. / Loiodice, F. #1: Journal: J.Med.Chem. / Year: 2008 Title: Crystal structure of the peroxisome proliferator-activated receptor gamma (PPARgamma) ligand binding domain complexed with a novel partial agonist: a new region of the hydrophobic pocket could ...Title: Crystal structure of the peroxisome proliferator-activated receptor gamma (PPARgamma) ligand binding domain complexed with a novel partial agonist: a new region of the hydrophobic pocket could be exploited for drug design Authors: Montanari, R. / Saccoccia, F. / Scotti, E. / Crestani, M. / Godio, C. / Gilardi, F. / Loiodice, F. / Fracchiolla, G. / Laghezza, A. / Tortorella, P. / Lavecchia, A. / Novellino, E. / Mazza, ...Authors: Montanari, R. / Saccoccia, F. / Scotti, E. / Crestani, M. / Godio, C. / Gilardi, F. / Loiodice, F. / Fracchiolla, G. / Laghezza, A. / Tortorella, P. / Lavecchia, A. / Novellino, E. / Mazza, F. / Aschi, M. / Pochetti, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ho0.cif.gz | 121 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ho0.ent.gz | 94.3 KB | Display | PDB format |
PDBx/mmJSON format | 3ho0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ho0_validation.pdf.gz | 696.3 KB | Display | wwPDB validaton report |
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Full document | 3ho0_full_validation.pdf.gz | 717.3 KB | Display | |
Data in XML | 3ho0_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 3ho0_validation.cif.gz | 32.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ho/3ho0 ftp://data.pdbj.org/pub/pdb/validation_reports/ho/3ho0 | HTTPS FTP |
-Related structure data
Related structure data | 3hodC 3b3kS 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: 32530.652 Da / Num. of mol.: 2 / Fragment: ligand binding domain (LBD), UNP residues 223-504 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37231 #2: Chemical | ChemComp-DKD / ( | #3: 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: 2.62 Å3/Da / Density % sol: 53.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.8M NaCitrate, 0.15M Tris, pH8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 9, 2008 |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→25 Å / Num. obs: 20618 / % possible obs: 5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 68.4 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 1.9 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3B3K Resolution: 2.6→10 Å / Isotropic thermal model: Isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.6→10 Å
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Refine LS restraints |
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