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Yorodumi- PDB-5ml0: Bromodomain of Mouse PCAF with (R)-4-chloro-2-methyl-5-((1-methyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ml0 | ||||||
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Title | Bromodomain of Mouse PCAF with (R)-4-chloro-2-methyl-5-((1-methylpiperidin-3-yl)amino)pyridazin-3(2H)-one | ||||||
Components | Histone acetyltransferase KAT2B | ||||||
Keywords | TRANSCRIPTION / INHIBITOR / HISTONE / EPIGENETIC READER / BROMODOMAIN / PCAF / ANTAGONIST | ||||||
Function / homology | Function and homology information : / : / B-WICH complex positively regulates rRNA expression / YAP1- and WWTR1 (TAZ)-stimulated gene expression / : / : / Regulation of FOXO transcriptional activity by acetylation / : / regulation of protein ADP-ribosylation / negative regulation of rRNA processing ...: / : / B-WICH complex positively regulates rRNA expression / YAP1- and WWTR1 (TAZ)-stimulated gene expression / : / : / Regulation of FOXO transcriptional activity by acetylation / : / regulation of protein ADP-ribosylation / negative regulation of rRNA processing / Metalloprotease DUBs / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / Notch-HLH transcription pathway / : / diamine N-acetyltransferase / diamine N-acetyltransferase activity / negative regulation of centriole replication / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / peptidyl-lysine acetylation / Estrogen-dependent gene expression / actomyosin / internal peptidyl-lysine acetylation / negative regulation of cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein serine/threonine kinase inhibitor activity / N-terminal peptidyl-lysine acetylation / I band / positive regulation of chromatin binding / limb development / A band / histone acetyltransferase binding / peptide-lysine-N-acetyltransferase activity / protein acetylation / acetyltransferase activity / transcription factor binding / histone acetyltransferase complex / histone acetyltransferase activity / positive regulation of gluconeogenesis / histone acetyltransferase / transcription coregulator activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / positive regulation of neuron projection development / kinetochore / histone deacetylase binding / cellular response to insulin stimulus / rhythmic process / heart development / transcription coactivator activity / chromatin remodeling / cell cycle / negative regulation of cell population proliferation / centrosome / chromatin binding / chromatin / regulation of DNA-templated transcription / protein kinase binding / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.64 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 | 5ml0.cif.gz | 62.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ml0.ent.gz | 48.3 KB | Display | PDB format |
PDBx/mmJSON format | 5ml0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/5ml0 ftp://data.pdbj.org/pub/pdb/validation_reports/ml/5ml0 | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 13191.225 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kat2b, Pcaf / Production host: Escherichia coli (E. coli) / References: UniProt: Q9JHD1, histone acetyltransferase | ||
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#2: Chemical | ChemComp-P2L / | ||
#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: 2.12 Å3/Da / Density % sol: 42.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 30% P550MME P20K, 0.1M Morpheus buffer 3 pH8.5, 10% morpheus amino acids |
-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: Jul 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→30.39 Å / Num. obs: 12718 / % possible obs: 97 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.017 / Net I/σ(I): 50.7 |
Reflection shell | Resolution: 1.64→1.73 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.039 / Mean I/σ(I) obs: 20.8 / % possible all: 84.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→30.39 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.737 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.116 / 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: 25.439 Å2
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Refinement step | Cycle: LAST / Resolution: 1.64→30.39 Å
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Refine LS restraints |
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