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Yorodumi- PDB-5mkx: 1.68A STRUCTURE PCAF BROMODOMAIN WITH 4-chloro-2-methyl-5-(methyl... -
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-Basic information
Entry | Database: PDB / ID: 5mkx | ||||||
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Title | 1.68A STRUCTURE PCAF BROMODOMAIN WITH 4-chloro-2-methyl-5-(methylamino)pyridazin-3(2H)-one | ||||||
Components | Histone acetyltransferase KAT2B | ||||||
Keywords | TRANSCRIPTION / INHIBITOR / HISTONE / EPIGENETIC READER / BROMODOMAIN / PCAF / ANTAGONIST | ||||||
Function / homology | Function and homology information regulation of protein ADP-ribosylation / negative regulation of rRNA processing / histone H3K9 acetyltransferase activity / diamine N-acetyltransferase / diamine N-acetyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / negative regulation of centriole replication / Physiological factors / positive regulation of attachment of mitotic spindle microtubules to kinetochore / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor ...regulation of protein ADP-ribosylation / negative regulation of rRNA processing / histone H3K9 acetyltransferase activity / diamine N-acetyltransferase / diamine N-acetyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / negative regulation of centriole replication / Physiological factors / positive regulation of attachment of mitotic spindle microtubules to kinetochore / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / peptidyl-lysine acetylation / YAP1- and WWTR1 (TAZ)-stimulated gene expression / histone H3 acetyltransferase activity / positive regulation of fatty acid biosynthetic process / actomyosin / internal peptidyl-lysine acetylation / cyclin-dependent protein serine/threonine kinase inhibitor activity / ATAC complex / N-terminal peptidyl-lysine acetylation / I band / SAGA complex / cellular response to parathyroid hormone stimulus / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / limb development / RUNX3 regulates NOTCH signaling / A band / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of FOXO transcriptional activity by acetylation / NOTCH3 Intracellular Domain Regulates Transcription / histone acetyltransferase binding / peptide-lysine-N-acetyltransferase activity / regulation of tubulin deacetylation / regulation of cell division / Notch-HLH transcription pathway / Formation of WDR5-containing histone-modifying complexes / protein acetylation / regulation of RNA splicing / Formation of paraxial mesoderm / acetyltransferase activity / RNA Polymerase I Transcription Initiation / regulation of embryonic development / regulation of DNA repair / histone acetyltransferase activity / positive regulation of gluconeogenesis / histone acetyltransferase / transcription initiation-coupled chromatin remodeling / positive regulation of glycolytic process / gluconeogenesis / transcription coregulator activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / B-WICH complex positively regulates rRNA expression / positive regulation of neuron projection development / Metalloprotease DUBs / mitotic spindle / NOTCH1 Intracellular Domain Regulates Transcription / memory / kinetochore / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Pre-NOTCH Transcription and Translation / vasodilation / histone deacetylase binding / cellular response to insulin stimulus / rhythmic process / cellular response to oxidative stress / heart development / HATs acetylate histones / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription coactivator activity / regulation of cell cycle / chromatin remodeling / cell cycle / negative regulation of cell population proliferation / centrosome / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.68 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 | 5mkx.cif.gz | 109.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mkx.ent.gz | 86.9 KB | Display | PDB format |
PDBx/mmJSON format | 5mkx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mk/5mkx ftp://data.pdbj.org/pub/pdb/validation_reports/mk/5mkx | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 14172.371 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: SM first two residues left over from tag cleavage / Source: (gene. exp.) Homo sapiens (human) / Gene: KAT2B, PCAF / Production host: Escherichia coli (E. coli) / References: UniProt: Q92831, histone acetyltransferase |
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-Non-polymers , 5 types, 365 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-EPE / | #5: Chemical | ChemComp-BU1 / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.73 Å3/Da / Density % sol: 67.05 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / Details: Morpheus condition 37 |
-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: Jun 15, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→49.63 Å / Num. obs: 39507 / % possible obs: 94.2 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.026 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 1.68→1.77 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 3.6 / % possible all: 83.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.68→32.65 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.289 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.088 / 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: 30.631 Å2
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Refinement step | Cycle: LAST / Resolution: 1.68→32.65 Å
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