[English] 日本語
Yorodumi- PDB-6dgq: Crystal Structure of Human PPARgamma Ligand Binding Domain in Com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dgq | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Human PPARgamma Ligand Binding Domain in Complex with CAY10506 | ||||||
Components | Peroxisome proliferator-activated receptor gamma | ||||||
Keywords | TRANSCRIPTION/TRANSCRIPTION INHIBITOR / Nuclear receptors / TZDs / Drug design / Therapeutic targets / TRANSCRIPTION / TRANSCRIPTION-TRANSCRIPTION INHIBITOR complex | ||||||
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: 2.45 Å | ||||||
Authors | Shang, J. / Kojetin, D.J. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2019 Title: Quantitative structural assessment of graded receptor agonism. Authors: Shang, J. / Brust, R. / Griffin, P.R. / Kamenecka, T.M. / Kojetin, D.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6dgq.cif.gz | 118.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6dgq.ent.gz | 90.4 KB | Display | PDB format |
PDBx/mmJSON format | 6dgq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dgq_validation.pdf.gz | 717.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6dgq_full_validation.pdf.gz | 731.1 KB | Display | |
Data in XML | 6dgq_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | 6dgq_validation.cif.gz | 32.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dg/6dgq ftp://data.pdbj.org/pub/pdb/validation_reports/dg/6dgq | HTTPS FTP |
-Related structure data
Related structure data | 6dglC 6dgoC 6dgrC 6o67C 6o68C 1prgS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 31506.574 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Plasmid: pET46 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P37231 #2: Chemical | ChemComp-GBV / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.19 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.8M SODIUM CITRATE, 100mM Tris, pH 7.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97741 Å |
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: 2.45→45.48 Å / Num. obs: 22240 / % possible obs: 97.3 % / Redundancy: 2 % / CC1/2: 0.998 / Net I/σ(I): 12.38 |
Reflection shell | Resolution: 2.45→2.538 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.89 / Num. unique obs: 2193 / CC1/2: 0.811 / % possible all: 96.95 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PRG Resolution: 2.45→45.48 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.51
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→45.48 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|