+Open data
-Basic information
Entry | Database: PDB / ID: 5y8w | ||||||
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Title | Crystal Structure Analysis of the BRD4 | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | TRANSCRIPTION / BRD4(1) / Bromodomain | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.76 Å | ||||||
Authors | Xu, Y. / Zhang, Y. / Song, M. / Wang, C. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2018 Title: Structure-Based Discovery and Optimization of Benzo[ d]isoxazole Derivatives as Potent and Selective BET Inhibitors for Potential Treatment of Castration-Resistant Prostate Cancer (CRPC) Authors: Zhang, M. / Zhang, Y. / Song, M. / Xue, X. / Wang, J. / Wang, C. / Zhang, C. / Li, C. / Xiang, Q. / Zou, L. / Wu, X. / Wu, C. / Dong, B. / Xue, W. / Zhou, Y. / Chen, H. / Wu, D. / Ding, K. / Xu, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5y8w.cif.gz | 45 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y8w.ent.gz | 29.5 KB | Display | PDB format |
PDBx/mmJSON format | 5y8w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5y8w_validation.pdf.gz | 892.1 KB | Display | wwPDB validaton report |
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Full document | 5y8w_full_validation.pdf.gz | 892.2 KB | Display | |
Data in XML | 5y8w_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 5y8w_validation.cif.gz | 10.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/5y8w ftp://data.pdbj.org/pub/pdb/validation_reports/y8/5y8w | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 16767.326 Da / Num. of mol.: 1 / Fragment: UNP residues 44-168 Source method: isolated from a genetically manipulated source Details: sequence from 28-43 are tags. MKKGHHHHHHLVPRGS / Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O60885 |
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-Non-polymers , 6 types, 73 molecules
#2: Chemical | ChemComp-8PU / | ||||||||
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#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-NO3 / | #5: Chemical | ChemComp-NA / | #6: Chemical | ChemComp-GOL / | #7: 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: 2.22 Å3/Da / Density % sol: 44.67 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: 20% PEG3350, 0.2M NaNO3, 0.1M HEPES, 10% EtGhly,pH8.2 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→77.68 Å / Num. obs: 14984 / % possible obs: 99.8 % / Redundancy: 5.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.037 / Rrim(I) all: 0.089 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.76→1.8 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.48 / Num. unique obs: 833 / CC1/2: 0.952 / Rpim(I) all: 0.221 / Rrim(I) all: 0.531 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Resolution: 1.76→40.96 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.108 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.121 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.64 Å2 / Biso mean: 29.105 Å2 / Biso min: 15.84 Å2
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Refinement step | Cycle: final / Resolution: 1.76→40.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.764→1.81 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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