+Open data
-Basic information
Entry | Database: PDB / ID: 7riu | ||||||
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Title | human PXR LBD bound to GSK002 | ||||||
Components | Isoform 1C of Nuclear receptor subfamily 1 group I member 2 | ||||||
Keywords | GENE REGULATION / nuclear receptor / helical sandwhich | ||||||
Function / homology | Function and homology information xenobiotic transport / intermediate filament cytoskeleton / steroid metabolic process / xenobiotic catabolic process / xenobiotic metabolic process / SUMOylation of intracellular receptors / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Nuclear Receptor transcription pathway / nuclear receptor activity ...xenobiotic transport / intermediate filament cytoskeleton / steroid metabolic process / xenobiotic catabolic process / xenobiotic metabolic process / SUMOylation of intracellular receptors / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / 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 / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / positive regulation of gene expression / positive regulation of DNA-templated transcription / chromatin / 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 / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å | ||||||
Authors | Williams, S.P. / Wisely, G.B. / Ward, P. | ||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2021 Title: Overcoming the Pregnane X Receptor Liability: Rational Design to Eliminate PXR-Mediated CYP Induction. Authors: Ramanjulu, J.M. / Williams, S.P. / Lakdawala, A.S. / DeMartino, M.P. / Lan, Y. / Marquis, R.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7riu.cif.gz | 74.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7riu.ent.gz | 51.6 KB | Display | PDB format |
PDBx/mmJSON format | 7riu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ri/7riu ftp://data.pdbj.org/pub/pdb/validation_reports/ri/7riu | HTTPS FTP |
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-Related structure data
Related structure data | 7n2aC 7rioC 7rivC 1ilhS C: citing same article (ref.) 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: 34187.562 Da / Num. of mol.: 1 / Fragment: ligand binding domain 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-5YU / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.72 % / Mosaicity: 0.248 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 50mM Imidazole pH7.2, 12% 2-propanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 12, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. obs: 23743 / % possible obs: 94.5 % / Redundancy: 12.1 % / Biso Wilson estimate: 31.23 Å2 / Rmerge(I) obs: 0.092 / Χ2: 1.643 / Net I/σ(I): 8.7 / Num. measured all: 287822 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdbid 1ILH Resolution: 2.05→40.9 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.72 / 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: 120.62 Å2 / Biso mean: 36.3785 Å2 / Biso min: 15.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.05→40.9 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11
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