+Open data
-Basic information
Entry | Database: PDB / ID: 6p2b | ||||||
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Title | Tethered PXR-LBD/SRC-1p bound to Garcinoic Acid | ||||||
Components | Nuclear receptor subfamily 1 group I member 2 | ||||||
Keywords | TRANSCRIPTION / Garcinoic Acid / nuclear receptor | ||||||
Function / homology | Function and homology information xenobiotic transport / intermediate filament cytoskeleton / steroid metabolic process / xenobiotic catabolic process / xenobiotic metabolic process / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / nuclear receptor activity ...xenobiotic transport / intermediate filament cytoskeleton / steroid metabolic process / xenobiotic catabolic process / xenobiotic metabolic process / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / cell differentiation / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Walton, W.G. / Pellock, S.J. / Redinbo, M.R. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Med.Chem. / Year: 2020 Title: Garcinoic Acid Is a Natural and Selective Agonist of Pregnane X Receptor. Authors: Bartolini, D. / De Franco, F. / Torquato, P. / Marinelli, R. / Cerra, B. / Ronchetti, R. / Schon, A. / Fallarino, F. / De Luca, A. / Bellezza, G. / Ferri, I. / Sidoni, A. / Walton, W.G. / ...Authors: Bartolini, D. / De Franco, F. / Torquato, P. / Marinelli, R. / Cerra, B. / Ronchetti, R. / Schon, A. / Fallarino, F. / De Luca, A. / Bellezza, G. / Ferri, I. / Sidoni, A. / Walton, W.G. / Pellock, S.J. / Redinbo, M.R. / Mani, S. / Pellicciari, R. / Gioiello, A. / Galli, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6p2b.cif.gz | 137.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p2b.ent.gz | 104.9 KB | Display | PDB format |
PDBx/mmJSON format | 6p2b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p2/6p2b ftp://data.pdbj.org/pub/pdb/validation_reports/p2/6p2b | HTTPS FTP |
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-Related structure data
Related structure data | 3ctbS S: Starting model for refinement |
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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: 39184.035 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NR1I2, PXR / Production host: Escherichia coli (E. coli) / References: UniProt: O75469 #2: Chemical | #3: Chemical | #4: 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: 2.61 Å3/Da / Density % sol: 52.89 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 30% MPD, 100mM Imidazole, pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→29.63 Å / Num. obs: 36411 / % possible obs: 98.03 % / Redundancy: 5.2 % / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.3→2.382 Å / Num. unique obs: 3612 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CTB Resolution: 2.3→29.63 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.04
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→29.63 Å
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Refine LS restraints |
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LS refinement shell |
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