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Yorodumi- PDB-4lr6: Structure of BRD4 bromodomain 1 with a 3-methyl-4-phenylisoxazol-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lr6 | ||||||
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Title | Structure of BRD4 bromodomain 1 with a 3-methyl-4-phenylisoxazol-5-amine fragment | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | TRANSCRIPTION REGULATOR/INHIBITOR / BET inhibitor / Brd4 first bromodomain / TRANSCRIPTION REGULATOR-INHIBITOR complex | ||||||
Function / homology | Function and homology information RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II ...RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / lysine-acetylated histone binding / p53 binding / chromosome / regulation of inflammatory response / positive regulation of canonical NF-kappaB signal transduction / Potential therapeutics for SARS / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å | ||||||
Authors | Jayaram, H. / Poy, F. / Gehling, V. / Hewitt, M. / Vaswani, R. / Leblanc, Y. / Cote, A. / Nasveschuk, C. / Taylor, A. / Harmange, J.-C. ...Jayaram, H. / Poy, F. / Gehling, V. / Hewitt, M. / Vaswani, R. / Leblanc, Y. / Cote, A. / Nasveschuk, C. / Taylor, A. / Harmange, J.-C. / Audia, J. / Pardo, E. / Joshi, S. / Sandy, P. / Mertz, J. / Sims, R. / Bergeron, L. / Bryant, B. / Ravichandran, S. / Yellapuntala, S. / Nandana, B.S. / Birudukota, S. / Albrecht, B. / Bellon, S. | ||||||
Citation | Journal: ACS Med Chem Lett / Year: 2013 Title: Discovery, Design, and Optimization of Isoxazole Azepine BET Inhibitors. Authors: Gehling, V.S. / Hewitt, M.C. / Vaswani, R.G. / Leblanc, Y. / Cote, A. / Nasveschuk, C.G. / Taylor, A.M. / Harmange, J.C. / Audia, J.E. / Pardo, E. / Joshi, S. / Sandy, P. / Mertz, J.A. / ...Authors: Gehling, V.S. / Hewitt, M.C. / Vaswani, R.G. / Leblanc, Y. / Cote, A. / Nasveschuk, C.G. / Taylor, A.M. / Harmange, J.C. / Audia, J.E. / Pardo, E. / Joshi, S. / Sandy, P. / Mertz, J.A. / Sims, R.J. / Bergeron, L. / Bryant, B.M. / Bellon, S. / Poy, F. / Jayaram, H. / Sankaranarayanan, R. / Yellapantula, S. / Bangalore Srinivasamurthy, N. / Birudukota, S. / Albrecht, B.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lr6.cif.gz | 69.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lr6.ent.gz | 50.6 KB | Display | PDB format |
PDBx/mmJSON format | 4lr6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lr6_validation.pdf.gz | 445.4 KB | Display | wwPDB validaton report |
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Full document | 4lr6_full_validation.pdf.gz | 445.7 KB | Display | |
Data in XML | 4lr6_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 4lr6_validation.cif.gz | 10.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lr/4lr6 ftp://data.pdbj.org/pub/pdb/validation_reports/lr/4lr6 | HTTPS FTP |
-Related structure data
Related structure data | 4lrgC 3mxfS 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: 15126.339 Da / Num. of mol.: 1 / Fragment: bromodomain 1 (UNP residues 42-168) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, BRD4_HUMAN, HUNK1 / Plasmid: pRSF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Rosetta2 / References: UniProt: O60885 | ||||
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#2: Chemical | #3: Chemical | ChemComp-1XA / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.19 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 3.682 M Formate, 10% Glycerol, 0.1 M Tris-HCl pH 8.5, vapor diffusion, sitting drop, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1 Å |
Detector | Detector: CCD / Date: Jan 1, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50 Å / Num. obs: 29117 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MXF Resolution: 1.29→30.13 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.934 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 78.06 Å2 / Biso mean: 24.373 Å2 / Biso min: 14.09 Å2
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Refinement step | Cycle: LAST / Resolution: 1.29→30.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.289→1.323 Å / Total num. of bins used: 20
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