+Open data
-Basic information
Entry | Database: PDB / ID: 6cks | ||||||
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Title | Crystal Structure of BRD4 with QC4956 | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | GENE REGULATION/INHIBITOR / BRD4 / Acetyllysine / epigenetics / GENE REGULATION-INHIBITOR complex | ||||||
Function / homology | Amanitin/phalloidin toxin / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / toxin activity / Up-down Bundle / Mainly Alpha / Chem-F5Y / Alpha-amanitin proprotein 1 Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å | ||||||
Authors | Hosfield, D.J. | ||||||
Citation | Journal: Bioorg. Med. Chem. Lett. / Year: 2018 Title: Design, synthesis and biological evaluation of novel 4-phenylisoquinolinone BET bromodomain inhibitors. Authors: Bennett, M.J. / Wu, Y. / Boloor, A. / Matuszkiewicz, J. / O'Connell, S.M. / Shi, L. / Stansfield, R.K. / Del Rosario, J.R. / Veal, J.M. / Hosfield, D.J. / Xu, J. / Kaldor, S.W. / Stafford, J.A. / Betancort, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cks.cif.gz | 46.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cks.ent.gz | 29.8 KB | Display | PDB format |
PDBx/mmJSON format | 6cks.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cks_validation.pdf.gz | 751.7 KB | Display | wwPDB validaton report |
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Full document | 6cks_full_validation.pdf.gz | 753.3 KB | Display | |
Data in XML | 6cks_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 6cks_validation.cif.gz | 13.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/6cks ftp://data.pdbj.org/pub/pdb/validation_reports/ck/6cks | HTTPS FTP |
-Related structure data
Related structure data | 6ckrC 5f63S 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: 15012.301 Da / Num. of mol.: 1 / Fragment: UNP residues 44-168 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: O60885 |
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#2: Chemical | ChemComp-F5Y / |
#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: 1.94 Å3/Da / Density % sol: 36.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20% PEG6000, 50 mM TRIS, pH 7.7, 5% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 80 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 27, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.72→30 Å / Num. obs: 12897 / % possible obs: 99.3 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.07 / Χ2: 1.046 / Net I/σ(I): 10.1 / Num. measured all: 73555 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5F63 Resolution: 1.72→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.46 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.119 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 63.55 Å2 / Biso mean: 19.827 Å2 / Biso min: 10.29 Å2
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Refinement step | Cycle: final / Resolution: 1.72→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.717→1.762 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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