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Yorodumi- PDB-5mkz: N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 4-chloro-2-methyl-5-(((... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mkz | ||||||
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Title | N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 4-chloro-2-methyl-5-(((3-methylthiophen-2-yl)methyl)amino)pyridazin-3(2H)-one | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | TRANSCRIPTION / INHIBITOR / HISTONE / EPIGENETIC READER / BROMODOMAIN / BRD4 / BROMODOMAIN CONTAINING PROTEIN 4 / ANTAGONIST | ||||||
Function / homology | Amanitin/phalloidin toxin / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / toxin activity / Up-down Bundle / Mainly Alpha / Chem-RNK / Alpha-amanitin proprotein 1 Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | ||||||
Authors | Chung, C.-W. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2017 Title: Discovery of a Potent, Cell Penetrant, and Selective p300/CBP-Associated Factor (PCAF)/General Control Nonderepressible 5 (GCN5) Bromodomain Chemical Probe. Authors: Humphreys, P.G. / Bamborough, P. / Chung, C.W. / Craggs, P.D. / Gordon, L. / Grandi, P. / Hayhow, T.G. / Hussain, J. / Jones, K.L. / Lindon, M. / Michon, A.M. / Renaux, J.F. / Suckling, C.J. ...Authors: Humphreys, P.G. / Bamborough, P. / Chung, C.W. / Craggs, P.D. / Gordon, L. / Grandi, P. / Hayhow, T.G. / Hussain, J. / Jones, K.L. / Lindon, M. / Michon, A.M. / Renaux, J.F. / Suckling, C.J. / Tough, D.F. / Prinjha, R.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mkz.cif.gz | 49.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mkz.ent.gz | 34.2 KB | Display | PDB format |
PDBx/mmJSON format | 5mkz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mkz_validation.pdf.gz | 789.5 KB | Display | wwPDB validaton report |
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Full document | 5mkz_full_validation.pdf.gz | 789.5 KB | Display | |
Data in XML | 5mkz_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 5mkz_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mk/5mkz ftp://data.pdbj.org/pub/pdb/validation_reports/mk/5mkz | 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
#1: Protein | Mass: 15099.380 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: SM left over from tag cleavage / 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-RNK / | ||
#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: 2.14 Å3/Da / Density % sol: 42.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M Sodium nitrate 0.1 M Bis Tris propane pH 6.5 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Apr 29, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→44.24 Å / Num. obs: 16730 / % possible obs: 97.3 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.026 / Net I/σ(I): 34.8 |
Reflection shell | Resolution: 1.62→1.7 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.106 / Mean I/σ(I) obs: 10.4 / % possible all: 83.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→15.21 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.598 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.085 / 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 mean: 13.387 Å2
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Refinement step | Cycle: LAST / Resolution: 1.62→15.21 Å
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Refine LS restraints |
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