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Yorodumi- PDB-6cd4: Crystal Structure of the first bromodomain of human BRD4 in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cd4 | |||||||||
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Title | Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor JWG046 | |||||||||
Components | Bromodomain-containing protein 4 | |||||||||
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 / chromatin / 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: 1.23 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 | 6cd4.cif.gz | 94.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cd4.ent.gz | 71.3 KB | Display | PDB format |
PDBx/mmJSON format | 6cd4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cd4_validation.pdf.gz | 765.4 KB | Display | wwPDB validaton report |
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Full document | 6cd4_full_validation.pdf.gz | 766.1 KB | Display | |
Data in XML | 6cd4_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 6cd4_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/6cd4 ftp://data.pdbj.org/pub/pdb/validation_reports/cd/6cd4 | HTTPS FTP |
-Related structure data
Related structure data | 5wa5C 6cd5C 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: 15069.286 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-EX1 / | ||
#3: Chemical | #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: 2.09 Å3/Da / Density % sol: 41.06 % |
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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-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 22, 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: 1.23→56.62 Å / Num. obs: 35971 / % possible obs: 96.3 % / Redundancy: 5.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.019 / Rrim(I) all: 0.047 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.23→1.25 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1093 / CC1/2: 0.478 / Rpim(I) all: 0.475 / Rrim(I) all: 0.846 / % possible all: 60.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WIV Resolution: 1.23→38.09 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.06
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.23→38.09 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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