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- PDB-8fpe: Crystal structure of pregnane X receptor ligand binding domain co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8fpe | ||||||
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Title | Crystal structure of pregnane X receptor ligand binding domain complexed with T0901317 analog T0-BP | ||||||
![]() | Nuclear receptor subfamily 1 group I member 2 | ||||||
![]() | TRANSCRIPTION / nuclear receptor / transcription factor / metabolism / antibiotic | ||||||
Function / homology | ![]() 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 / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huber, A.D. / Poudel, S. / Seetharaman, J. / Miller, D.J. / Lin, W. / Li, Y. / Chen, T. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73 KB | Display | ![]() |
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PDB format | ![]() | 50.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 765.5 KB | Display | ![]() |
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Full document | ![]() | 767.3 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Data in CIF | ![]() | 15.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8e3nC ![]() 8eqzC ![]() 1m13S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36208.742 Da / Num. of mol.: 1 / Fragment: UNP residues 153-457 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-Y5B / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 50 mM imidazole pH 7, 12% isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 18, 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: 2.3→36.76 Å / Num. obs: 16633 / % possible obs: 99.9 % / Redundancy: 14.7 % / Biso Wilson estimate: 49.81 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.03 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 15.2 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1591 / CC1/2: 0.815 / Rpim(I) all: 0.331 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1M13 Resolution: 2.3→35.54 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.8927 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: 55.93 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→35.54 Å
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Refine LS restraints |
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LS refinement shell |
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