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Yorodumi- PDB-8eqz: Crystal structure of pregnane X receptor ligand binding domain co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8eqz | ||||||
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Title | Crystal structure of pregnane X receptor ligand binding domain complexed with T0901317 analog T0-C6 | ||||||
Components | Nuclear receptor subfamily 1 group I member 2 | ||||||
Keywords | TRANSCRIPTION / nuclear receptor / transcription factor / metabolism / antibiotic | ||||||
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 / Resolution: 2.37 Å | ||||||
Authors | Huber, A.D. / Poudel, S. / Seetharaman, J. / Miller, D.J. / Lin, W. / Li, Y. / Chen, T. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2023 Title: Structure-guided approach to modulate small molecule binding to a promiscuous ligand-activated protein. Authors: Lin, W. / Huber, A.D. / Poudel, S. / Li, Y. / Seetharaman, J. / Miller, D.J. / Chen, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8eqz.cif.gz | 137 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8eqz.ent.gz | 101.9 KB | Display | PDB format |
PDBx/mmJSON format | 8eqz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/8eqz ftp://data.pdbj.org/pub/pdb/validation_reports/eq/8eqz | HTTPS FTP |
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-Related structure data
Related structure data | 8e3nC 8fpeC 3ctbS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 40342.242 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: 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: 2.49 Å3/Da / Density % sol: 50.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: 100 mM Bis-Tris (pH 5.8), 9% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 27, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9201 Å / Relative weight: 1 |
Reflection | Resolution: 2.37→29.67 Å / Num. obs: 33262 / % possible obs: 99.4 % / Redundancy: 6.8 % / Biso Wilson estimate: 50.75 Å2 / CC1/2: 0.998 / Rsym value: 0.081 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.37→2.43 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2244 / CC1/2: 0.749 / Rsym value: 0.758 / % possible all: 93.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CTB Resolution: 2.37→29.57 Å / SU ML: 0.2715 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.5115 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 60.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.37→29.57 Å
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Refine LS restraints |
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LS refinement shell |
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