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Yorodumi- PDB-1n46: CRYSTAL STRUCTURE OF HUMAN TR BETA LIGAND-BINDING DOMAIN COMPLEXE... -
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-Basic information
Entry | Database: PDB / ID: 1n46 | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN TR BETA LIGAND-BINDING DOMAIN COMPLEXED WITH A POTENT SUBTYPE-SELECTIVE THYROMIMETIC | ||||||
Components | Thyroid hormone receptor Beta-1 | ||||||
Keywords | TRANSCRIPTION | ||||||
Function / homology | Function and homology information retinal cone cell apoptotic process / negative regulation of female receptivity / female courtship behavior / retinal cone cell development / thyroid hormone mediated signaling pathway / positive regulation of thyroid hormone mediated signaling pathway / cellular response to thyroid hormone stimulus / regulation of heart contraction / type I pneumocyte differentiation / thyroid hormone binding ...retinal cone cell apoptotic process / negative regulation of female receptivity / female courtship behavior / retinal cone cell development / thyroid hormone mediated signaling pathway / positive regulation of thyroid hormone mediated signaling pathway / cellular response to thyroid hormone stimulus / regulation of heart contraction / type I pneumocyte differentiation / thyroid hormone binding / retinoic acid receptor signaling pathway / sensory perception of sound / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / transcription coactivator binding / chromatin DNA binding / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / cell differentiation / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Dow, R.L. / Schneider, S.R. / Paight, E.S. / Hank, R.F. / Chiang, P. / Cornelius, P. / Lee, E. / Newsome, W.P. / Swick, A.G. / Spitzer, J. ...Dow, R.L. / Schneider, S.R. / Paight, E.S. / Hank, R.F. / Chiang, P. / Cornelius, P. / Lee, E. / Newsome, W.P. / Swick, A.G. / Spitzer, J. / Hargrove, D.M. / Patterson, T.A. / Pandit, J. / Chrunyk, B.A. / LeMotte, P.K. / Danley, D.E. / Rosner, M.H. / Ammirati, M.J. / Simons, S.P. / Schulte, G.K. / Tate, B.F. / DaSilva-Jardine, P. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2003 Title: Discovery of a Novel Series of 6-Azauracil-Based Thyroid Hormone Receptor Ligands: Potent, TRbeta Subtype-Selective Thyromimetics Authors: Dow, R.L. / Schneider, S.R. / Paight, E.S. / Hank, R.F. / Chiang, P. / Cornelius, P. / Lee, E. / Newsome, W.P. / Swick, A.G. / Spitzer, J. / Hargrove, D.M. / Patterson, T.A. / Pandit, J. / ...Authors: Dow, R.L. / Schneider, S.R. / Paight, E.S. / Hank, R.F. / Chiang, P. / Cornelius, P. / Lee, E. / Newsome, W.P. / Swick, A.G. / Spitzer, J. / Hargrove, D.M. / Patterson, T.A. / Pandit, J. / Chrunyk, B.A. / LeMotte, P.K. / Danley, D.E. / Rosner, M.H. / Ammirati, M.J. / Simons, S.P. / Schulte, G.K. / Tate, B.F. / DaSilva-Jardine, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n46.cif.gz | 111.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n46.ent.gz | 85.8 KB | Display | PDB format |
PDBx/mmJSON format | 1n46.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n4/1n46 ftp://data.pdbj.org/pub/pdb/validation_reports/n4/1n46 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 5
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-Components
#1: Protein | Mass: 29152.773 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P10828 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.21 Å3/Da / Density % sol: 44.02 % | ||||||||||||||||||
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Crystal grow | pH: 6 / Details: pH 6.0, temperature 100K | ||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE |
Radiation | Monochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 22969 / Observed criterion σ(I): -3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.886 / SU B: 6.808 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.335 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.999 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20 /
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Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |