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Yorodumi- PDB-5eis: FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4 IN COMPLEX WITH INHIBITOR ... -
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-Basic information
Entry | Database: PDB / ID: 5eis | ||||||
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Title | FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4 IN COMPLEX WITH INHIBITOR 3-(4-Chlorobenzyl)-7-ethyl-3,7-dihydropurine-2,6-dione | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | TRANSCRIPTION / INHIBITOR / HISTONE / EPIGENETIC READER / BROMODOMAIN / 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: 1.6 Å | ||||||
Authors | Raux, B. / Rebuffet, E. / Betzi, S. / Morelli, X. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2016 Title: Exploring Selective Inhibition of the First Bromodomain of the Human Bromodomain and Extra-terminal Domain (BET) Proteins. Authors: Raux, B. / Voitovich, Y. / Derviaux, C. / Lugari, A. / Rebuffet, E. / Milhas, S. / Priet, S. / Roux, T. / Trinquet, E. / Guillemot, J.C. / Knapp, S. / Brunel, J.M. / Fedorov, A.Y. / ...Authors: Raux, B. / Voitovich, Y. / Derviaux, C. / Lugari, A. / Rebuffet, E. / Milhas, S. / Priet, S. / Roux, T. / Trinquet, E. / Guillemot, J.C. / Knapp, S. / Brunel, J.M. / Fedorov, A.Y. / Collette, Y. / Roche, P. / Betzi, S. / Combes, S. / Morelli, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5eis.cif.gz | 44.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eis.ent.gz | 29.8 KB | Display | PDB format |
PDBx/mmJSON format | 5eis.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/5eis ftp://data.pdbj.org/pub/pdb/validation_reports/ei/5eis | HTTPS FTP |
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-Related structure data
Related structure data | 5eguC 5ei4C 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 44-168 / Mutation: NO Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / References: UniProt: O60885 | ||
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#2: Chemical | ChemComp-5OU / | ||
#3: Chemical | Mass: 62.068 Da / Num. of mol.: 2 / Fragment: N-TERMINAL BROMODOMAIN, RESIDUES 42-168 / Mutation: NO Source method: isolated from a genetically manipulated source Formula: C2H6O2 / Source: (gene. exp.) Homo sapiens (human) / Gene: 19p13.12 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) #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: 2.15 Å3/Da / Density % sol: 42.9 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop Details: ratio 1:1 (protein:precipitant). 16 mg/mL Brd4_BD1 protein. 2.5 mM inhibitor (in DMSO) final concentration. Protein buffer: 0.1M HEPES (pH 7.5) 0.15 mM NaCl. Precipitant agent: 19% (w/v) PEG ...Details: ratio 1:1 (protein:precipitant). 16 mg/mL Brd4_BD1 protein. 2.5 mM inhibitor (in DMSO) final concentration. Protein buffer: 0.1M HEPES (pH 7.5) 0.15 mM NaCl. Precipitant agent: 19% (w/v) PEG 3350, 0.25M ammonium sulfate, 0.1M Tris pH 8.5. Cryoprotectant: 10% (w/v) ethylene glycol |
-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, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 17766 / % possible obs: 99.4 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 14.87 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 2.73 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OSS Resolution: 1.6→39.92 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.975 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.095 / 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: 27.433 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→39.92 Å
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