+Open data
-Basic information
Entry | Database: PDB / ID: 6hj2 | ||||||||||||||||||
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Title | Crystal structure of hPXR in complex with dabrafenib | ||||||||||||||||||
Components | Nuclear receptor subfamily 1 group I member 2 | ||||||||||||||||||
Keywords | NUCLEAR PROTEIN / pregnane X receptor anti-cancer drug endocrine disruptor 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: 2.28 Å | ||||||||||||||||||
Authors | Granell, M. / Delfosse, V. / Bourguet, W. | ||||||||||||||||||
Funding support | France, 5items
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Citation | Journal: To Be Published Title: Crystal structure of hPXR in complex with dabrafenib Authors: Granell, M. / Delfosse, V. / Bourguet, W. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hj2.cif.gz | 73.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hj2.ent.gz | 52 KB | Display | PDB format |
PDBx/mmJSON format | 6hj2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hj/6hj2 ftp://data.pdbj.org/pub/pdb/validation_reports/hj/6hj2 | HTTPS FTP |
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-Related structure data
Related structure data | 4x1fS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 36193.793 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NR1I2, PXR / Plasmid: PRSETA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O75469 |
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#2: Chemical | ChemComp-P06 / |
#3: Chemical | ChemComp-IPA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.97 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100 mM Imidazole 10% Isopropanol (dry co-crystallization with ligand) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→45.695 Å / Num. obs: 17136 / % possible obs: 100 % / Redundancy: 12.5 % / Rsym value: 0.06 / Net I/σ(I): 23.4 |
Reflection shell | Resolution: 2.28→2.34 Å / Redundancy: 12.8 % / Mean I/σ(I) obs: 5.2 / Num. unique obs: 1226 / Rsym value: 0.52 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4X1F Resolution: 2.28→45.695 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.67
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.28→45.695 Å
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Refine LS restraints |
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LS refinement shell |
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