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- PDB-8e3n: 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: 8e3n | ||||||
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Title | Crystal structure of pregnane X receptor ligand binding domain complexed with rifamycin S | ||||||
![]() | 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. / 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 | ![]() | 77.6 KB | Display | ![]() |
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PDB format | ![]() | 53 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 900.3 KB | Display | ![]() |
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Full document | ![]() | 902.9 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 18.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8eqzC ![]() 8fpeC ![]() 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-VA0 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 100 mM imidazole (pH 7.2), 14% 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: Feb 4, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→32.49 Å / Num. obs: 22158 / % possible obs: 99.6 % / Redundancy: 10.5 % / Biso Wilson estimate: 42.54 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.046 / Rrim(I) all: 0.148 / Rsym value: 0.092 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 2.2→2.26 Å / Num. unique obs: 1082 / CC1/2: 0.63 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1M13 Resolution: 2.25→32.49 Å / SU ML: 0.235 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 24.7104 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: 49.73 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→32.49 Å
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Refine LS restraints |
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LS refinement shell |
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