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Yorodumi- PDB-5dlz: FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4 IN COMPLEX WITH INHIBITOR ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dlz | ||||||
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Title | FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4 IN COMPLEX WITH INHIBITOR 4-[(1-methyl-2-oxo-1,2-dihydroquinolin-4-yl)oxy]-N-({1-[(3-methylphe methyl]piperidin-4-yl}methyl)butanamide | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | TRANSCRIPTION / INHIBITOR / HISTONE / EPIGENETIC READER / BROMODOMAIN / BRD4 / Brd4_BD1 | ||||||
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: 1.7 Å | ||||||
Authors | Raux, B. / Rebuffet, E. / Betzi, S. / Morelli, X. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2016 Title: Protein-Protein Interaction Inhibition (2P2I)-Oriented Chemical Library Accelerates Hit Discovery. Authors: Milhas, S. / Raux, B. / Betzi, S. / Derviaux, C. / Roche, P. / Restouin, A. / Basse, M.J. / Rebuffet, E. / Lugari, A. / Badol, M. / Kashyap, R. / Lissitzky, J.C. / Eydoux, C. / Hamon, V. / ...Authors: Milhas, S. / Raux, B. / Betzi, S. / Derviaux, C. / Roche, P. / Restouin, A. / Basse, M.J. / Rebuffet, E. / Lugari, A. / Badol, M. / Kashyap, R. / Lissitzky, J.C. / Eydoux, C. / Hamon, V. / Gourdel, M.E. / Combes, S. / Zimmermann, P. / Aurrand-Lions, M. / Roux, T. / Rogers, C. / Muller, S. / Knapp, S. / Trinquet, E. / Collette, Y. / Guillemot, J.C. / Morelli, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dlz.cif.gz | 69.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dlz.ent.gz | 50.4 KB | Display | PDB format |
PDBx/mmJSON format | 5dlz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dlz_validation.pdf.gz | 670.1 KB | Display | wwPDB validaton report |
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Full document | 5dlz_full_validation.pdf.gz | 670.7 KB | Display | |
Data in XML | 5dlz_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 5dlz_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/5dlz ftp://data.pdbj.org/pub/pdb/validation_reports/dl/5dlz | HTTPS FTP |
-Related structure data
Related structure data | 5dlxC 2ossS S: Starting model for refinement C: citing same article (ref.) |
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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: 15099.380 Da / Num. of mol.: 1 / Fragment: N-TERMINAL BROMODOMAIN, RESIDUES 42-168 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Plasmid: PLASMID / Details (production host): pDEST17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): star / References: UniProt: O60885 |
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#2: Chemical | ChemComp-5D1 / |
#3: 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: 2.15 Å3/Da / Density % sol: 42.92 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Ratio 1:1 (protein:precipitant) 12 mg/mL Brd4_BD1 protein. Protein buffer 10 mM HEPES (pH 7.5) 150 mM NaCl.Precipitant agent 22 % (w/v) PEG 3350, 10% (w/v) ethylene glycol 30 % (w/v), 0.3 M ...Details: Ratio 1:1 (protein:precipitant) 12 mg/mL Brd4_BD1 protein. Protein buffer 10 mM HEPES (pH 7.5) 150 mM NaCl.Precipitant agent 22 % (w/v) PEG 3350, 10% (w/v) ethylene glycol 30 % (w/v), 0.3 M NaNO3. 5.0 mM inhibitor (in DMSO) final concentration. Cryoprotection with 10% (w/v) glycerol. PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 15, 2006 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 14342 / % possible obs: 96.3 % / Redundancy: 4.47 % / Rsym value: 0.149 / Net I/σ(I): 7.54 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 4.38 % / Mean I/σ(I) obs: 4.15 / Rsym value: 0.421 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OSS Resolution: 1.7→39.22 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.83 / SU B: 11.321 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.253 / ESU R Free: 0.168 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.795 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→39.22 Å
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