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- PDB-6yqp: Crystal structure of the first bromodomain of human BRD4 in compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6yqp | ||||||
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Title | Crystal structure of the first bromodomain of human BRD4 in complex with the dual inhibitor TW22 | ||||||
![]() | Bromodomain-containing protein 4 | ||||||
![]() | GENE REGULATION / bromodomain / BRD4(BD1) / dual bromodomain HDAC inhibitor / structural genomics consortium / SGC | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joerger, A.C. / Balourdas, D.I. / Weiser, T. / Chatterjee, D. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Characterization of a dual BET/HDAC inhibitor for treatment of pancreatic ductal adenocarcinoma. Authors: Zhang, X. / Zegar, T. / Weiser, T. / Hamdan, F.H. / Berger, B.T. / Lucas, R. / Balourdas, D.I. / Ladigan, S. / Cheung, P.F. / Liffers, S.T. / Trajkovic-Arsic, M. / Scheffler, B. / Joerger, A. ...Authors: Zhang, X. / Zegar, T. / Weiser, T. / Hamdan, F.H. / Berger, B.T. / Lucas, R. / Balourdas, D.I. / Ladigan, S. / Cheung, P.F. / Liffers, S.T. / Trajkovic-Arsic, M. / Scheffler, B. / Joerger, A.C. / Hahn, S.A. / Johnsen, S.A. / Knapp, S. / Siveke, J.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 | ![]() | 87.6 KB | Display | ![]() |
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PDB format | ![]() | 54.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6yqnC ![]() 6yqoC ![]() 3mxfS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 15099.380 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-P8N / (~{ | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.68 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: Protein solution: 10 mg/ml in 10 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM TCEP, and 5% glycerol. 50 mM stock solution of TW22 in DMSO added to give a final inhibitor concentration 1.5 mM. ...Details: Protein solution: 10 mg/ml in 10 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM TCEP, and 5% glycerol. 50 mM stock solution of TW22 in DMSO added to give a final inhibitor concentration 1.5 mM. Reservoir buffer: 24% PEG 3350, 0.2 M sodium formate, 15 % ethylene glycol and 0.1 M bis-Tris-propane pH 7.9 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 30, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.70848 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→78.8 Å / Num. obs: 36807 / % possible obs: 99.9 % / Redundancy: 7.5 % / Biso Wilson estimate: 11.4566804012 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.25→1.27 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1827 / CC1/2: 0.884 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3MXF Resolution: 1.25→39.4 Å / SU ML: 0.122012427453 / Cross valid method: FREE R-VALUE / σ(F): 1.3364886602 / Phase error: 19.2307737008
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.1780030032 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→39.4 Å
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Refine LS restraints |
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LS refinement shell |
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