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Yorodumi- PDB-6cd5: Crystal Structure of the first bromodomain of human BRD4 in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cd5 | |||||||||
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Title | Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor XMD17-26 | |||||||||
Components | Bromodomain-containing protein 4BRD4 | |||||||||
Keywords | TRANSCRIPTION/INHIBITOR / Kinase / Inhibitor / BRD4 / TRANSCRIPTION / TRANSCRIPTION-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: 1.58 Å | |||||||||
Authors | Xu, X. / Blacklow, S.C. | |||||||||
Funding support | United States, 2items
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Citation | Journal: ACS Chem. Biol. / Year: 2018 Title: Structural and Atropisomeric Factors Governing the Selectivity of Pyrimido-benzodiazipinones as Inhibitors of Kinases and Bromodomains. Authors: Wang, J. / Erazo, T. / Ferguson, F.M. / Buckley, D.L. / Gomez, N. / Munoz-Guardiola, P. / Dieguez-Martinez, N. / Deng, X. / Hao, M. / Massefski, W. / Fedorov, O. / Offei-Addo, N.K. / Park, P. ...Authors: Wang, J. / Erazo, T. / Ferguson, F.M. / Buckley, D.L. / Gomez, N. / Munoz-Guardiola, P. / Dieguez-Martinez, N. / Deng, X. / Hao, M. / Massefski, W. / Fedorov, O. / Offei-Addo, N.K. / Park, P.M. / Dai, L. / DiBona, A. / Becht, K. / Kim, N.D. / McKeown, M.R. / Roberts, J.M. / Zhang, J. / Sim, T. / Alessi, D.R. / Bradner, J.E. / Lizcano, J.M. / Blacklow, S.C. / Qi, J. / Xu, X. / Gray, N.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cd5.cif.gz | 75.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cd5.ent.gz | 53.6 KB | Display | PDB format |
PDBx/mmJSON format | 6cd5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/6cd5 ftp://data.pdbj.org/pub/pdb/validation_reports/cd/6cd5 | HTTPS FTP |
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-Related structure data
Related structure data | 5wa5C 6cd4C 6cisC 6ciyC 6cj1C 6cj2C 4wivS 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: residues 44-168 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60885 | ||||
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#2: Chemical | ChemComp-R4L / | ||||
#3: Chemical | #4: Chemical | ChemComp-NO3 / | #5: 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: 2.38 Å3/Da / Density % sol: 48.4 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion Details: 100mM Sodium Nitrate, 5% Ethylene Glycol, 18% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→84.88 Å / Num. obs: 20478 / % possible obs: 100 % / Redundancy: 5.9 % / CC1/2: 0.935 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.167 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 1.58→1.61 Å / Redundancy: 6 % / Rmerge(I) obs: 0.634 / Num. unique obs: 991 / CC1/2: 0.623 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WIV Resolution: 1.58→36.272 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.32
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.58→36.272 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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