+Open data
-Basic information
Entry | Database: PDB / ID: 5z5u | ||||||
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Title | The first bromodomain of BRD4 with compound BDF-2254 | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | TRANSCRIPTION/INHIBITOR / BRD4 / Inhibitor / Complex / PROTEIN BINDING / 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: 1.631 Å | ||||||
Authors | Zhang, H. / Luo, C. | ||||||
Citation | Journal: Oncogenesis / Year: 2018 Title: Development and evaluation of a novel series of Nitroxoline-derived BET inhibitors with antitumor activity in renal cell carcinoma. Authors: Chen, W. / Zhang, H. / Chen, Z. / Jiang, H. / Liao, L. / Fan, S. / Xing, J. / Xie, Y. / Chen, S. / Ding, H. / Chen, K. / Jiang, H. / Luo, C. / Zheng, M. / Yao, Z. / Huang, Y. / Zhang, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5z5u.cif.gz | 44.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z5u.ent.gz | 28.9 KB | Display | PDB format |
PDBx/mmJSON format | 5z5u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5z5u_validation.pdf.gz | 428.9 KB | Display | wwPDB validaton report |
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Full document | 5z5u_full_validation.pdf.gz | 429.4 KB | Display | |
Data in XML | 5z5u_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 5z5u_validation.cif.gz | 12.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z5/5z5u ftp://data.pdbj.org/pub/pdb/validation_reports/z5/5z5u | HTTPS FTP |
-Related structure data
Related structure data | 5z5tC 5z5vC 5h21S 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: 14883.188 Da / Num. of mol.: 1 / Fragment: first bromodomain 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-96U / |
#3: 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 Å3/Da / Density % sol: 38.58 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 10-15% glycerol, 4M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 17, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1.631→40.54 Å / Num. obs: 15497 / % possible obs: 100 % / Redundancy: 2 % / Net I/σ(I): 21.69 |
Reflection shell | Resolution: 1.631→1.689 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5H21 Resolution: 1.631→40.539 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.21
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.631→40.539 Å
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Refine LS restraints |
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LS refinement shell |
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