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Yorodumi- PDB-5mky: BROMODOMAIN OF HUMAN BRD9 WITH 4-chloro-2-methyl-5-((2-methyl-1,2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mky | ||||||
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Title | BROMODOMAIN OF HUMAN BRD9 WITH 4-chloro-2-methyl-5-((2-methyl-1,2,3,4-tetrahydroisoquinolin-5-yl)amino)pyridazin-3(2H)-one | ||||||
Components | Bromodomain-containing protein 9 | ||||||
Keywords | TRANSCRIPTION / BRD9 / INHIBITOR / HISTONE / EPIGENETIC READER / BROMODOMAIN | ||||||
Function / homology | Function and homology information GBAF complex / SWI/SNF complex / positive regulation of stem cell population maintenance / negative regulation of cell differentiation / lysine-acetylated histone binding / nucleic acid binding / chromatin remodeling / chromatin / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II ...GBAF complex / SWI/SNF complex / positive regulation of stem cell population maintenance / negative regulation of cell differentiation / lysine-acetylated histone binding / nucleic acid binding / chromatin remodeling / chromatin / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.67 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 | 5mky.cif.gz | 57.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mky.ent.gz | 43.6 KB | Display | PDB format |
PDBx/mmJSON format | 5mky.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mk/5mky ftp://data.pdbj.org/pub/pdb/validation_reports/mk/5mky | HTTPS FTP |
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-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: 12228.203 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD9, UNQ3040/PRO9856 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H8M2 | ||
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#2: Chemical | #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: 2.49 Å3/Da / Density % sol: 50.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Morpheus condition 54 - 0.1M morpheus buffer 2 pH 7.5, 30% morpheus_EDO_P8K, 0.1M Morpheus ethylene glycols |
-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: Nov 11, 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: 1.67→36.48 Å / Num. obs: 11611 / % possible obs: 88.3 % / Redundancy: 2.19 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 1.67→1.73 Å / Redundancy: 1.83 % / Rmerge(I) obs: 0.119 / Mean I/σ(I) obs: 4.1 / % possible all: 85.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.67→36.48 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.935 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.123 / 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: 27.104 Å2
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Refinement step | Cycle: LAST / Resolution: 1.67→36.48 Å
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Refine LS restraints |
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