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- PDB-8zfo: Crystal Structure of Human PPARgamma Ligand Binding Domain in Com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8zfo | ||||||
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Title | Crystal Structure of Human PPARgamma Ligand Binding Domain in Complex with GW9662 and nTZDpa | ||||||
![]() | Peroxisome proliferator-activated receptor gamma | ||||||
![]() | TRANSCRIPTION / Nuclear receptors / TZDs / Drug design / Therapeutic targets | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shang, J. / Kojetin, D.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Unanticipated mechanisms of covalent inhibitor and synthetic ligand cobinding to PPAR gamma. Authors: Shang, J. / Kojetin, D.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 111.1 KB | Display | ![]() |
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PDB format | ![]() | 85.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 22.1 KB | Display | |
Data in CIF | ![]() | 29 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8zfnC ![]() 8zfpC ![]() 8zfqC ![]() 8zfrC ![]() 8zfsC ![]() 8zftC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 31449.520 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-GW9 / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: 0.8M SODIUM CITRATE, 100mM MOPS, pH 7.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 16, 2017 |
Radiation | Monochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97741 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→49.16 Å / Num. obs: 11672 / % possible obs: 99.59 % / Redundancy: 2 % / CC1/2: 0.998 / Net I/σ(I): 15.02 |
Reflection shell | Resolution: 3.15→3.263 Å / Redundancy: 2 % / Num. unique obs: 1161 / CC1/2: 0.916 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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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 max: 116.78 Å2 / Biso mean: 58.8147 Å2 / Biso min: 25.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.15→49.159 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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