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Yorodumi- PDB-5ovb: Crystal structure of human BRD4(1) bromodomain in complex with DR46 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ovb | ||||||
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Title | Crystal structure of human BRD4(1) bromodomain in complex with DR46 | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | DNA BINDING PROTEIN / BRD4 bromodomain 1(BRP4(1)) / Inhibitor | ||||||
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: 1.95 Å | ||||||
Authors | Zhu, J. / Caflisch, A. | ||||||
Citation | Journal: Acs Cent.Sci. / Year: 2018 Title: Chemical Space Expansion of Bromodomain Ligands Guided by in Silico Virtual Couplings (AutoCouple). Authors: Batiste, L. / Unzue, A. / Dolbois, A. / Hassler, F. / Wang, X. / Deerain, N. / Zhu, J. / Spiliotopoulos, D. / Nevado, C. / Caflisch, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ovb.cif.gz | 126.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ovb.ent.gz | 97.7 KB | Display | PDB format |
PDBx/mmJSON format | 5ovb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ovb_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5ovb_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5ovb_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 5ovb_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ov/5ovb ftp://data.pdbj.org/pub/pdb/validation_reports/ov/5ovb | HTTPS FTP |
-Related structure data
Related structure data | 5nlkC 5owmC 5owwC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15099.380 Da / Num. of mol.: 2 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 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.49 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M TRIS, pH 8.5, 0.2 M Ca Acet, 25% PEG 2K MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00004 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→46.75 Å / Num. obs: 21485 / % possible obs: 97.9 % / Redundancy: 3.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.155 / Num. unique obs: 1241 / CC1/2: 0.971 / % possible all: 81.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OSS Resolution: 1.95→46.75 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.4
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→46.75 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 11.9079 Å / Origin y: 43.184 Å / Origin z: 29.3489 Å
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Refinement TLS group | Selection details: all |