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Yorodumi- PDB-6zly: Crystal structure of the complex between PPARgamma LBD and the li... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zly | ||||||
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Title | Crystal structure of the complex between PPARgamma LBD and the ligand NV1362 (7a) | ||||||
Components | Peroxisome proliferator-activated receptor gamma | ||||||
Keywords | TRANSCRIPTION / TRANSCRIPTION FACTOR | ||||||
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: 1.79 Å | ||||||
Authors | Pochetti, G. / Montanari, R. / Capelli, D. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2020 Title: A Novel N-Substituted Valine Derivative with Unique Peroxisome Proliferator-Activated Receptor gamma Binding Properties and Biological Activities. Authors: Peiretti, F. / Montanari, R. / Capelli, D. / Bonardo, B. / Colson, C. / Amri, E.Z. / Grimaldi, M. / Balaguer, P. / Ito, K. / Roeder, R.G. / Pochetti, G. / Brunel, J.M. #1: Journal: J. Med. Chem. / Year: 2020 Title: Insights into PPARgamma Phosphorylation and Its Inhibition Mechanism Authors: Montanari, R. / Capelli, D. / Pochetti, G. / Itoh, T. / Yamamoto, K. / Loiodice, F. / Altieri, F. / Paiardini, A. / Grottesi, A. / Pedone, E. / Pirone, L. / Peiretti, F. / Brunel, J.M. / ...Authors: Montanari, R. / Capelli, D. / Pochetti, G. / Itoh, T. / Yamamoto, K. / Loiodice, F. / Altieri, F. / Paiardini, A. / Grottesi, A. / Pedone, E. / Pirone, L. / Peiretti, F. / Brunel, J.M. / Barendregt, A. / Heck, A.J.R. / Awaishima, H. / Nishikata, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zly.cif.gz | 116.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zly.ent.gz | 89 KB | Display | PDB format |
PDBx/mmJSON format | 6zly.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zly_validation.pdf.gz | 681.1 KB | Display | wwPDB validaton report |
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Full document | 6zly_full_validation.pdf.gz | 692.6 KB | Display | |
Data in XML | 6zly_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | 6zly_validation.cif.gz | 30.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/6zly ftp://data.pdbj.org/pub/pdb/validation_reports/zl/6zly | HTTPS FTP |
-Related structure data
Related structure data | 6qj5SC 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: 34220.504 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Production host: Escherichia coli (E. coli) / References: UniProt: P37231 #2: Chemical | ChemComp-QMH / ( | #3: 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: 2.34 Å3/Da / Density % sol: 47.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.8 M SODIUM CITRATE, 0.15 M TRIS, PH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.973 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 12, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.973 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→57.418 Å / Num. obs: 57534 / % possible obs: 96.5 % / Redundancy: 3.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.79→1.83 Å / Rmerge(I) obs: 1.138 / Num. unique obs: 3404 / CC1/2: 0.425 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6QJ5 Resolution: 1.79→57.418 Å / FOM work R set: 0.7202 / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 34.15 / Stereochemistry target values: ML
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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: 98.03 Å2 / Biso mean: 41.88 Å2 / Biso min: 20.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.79→57.418 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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