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Yorodumi- PDB-6oir: Crystal structure of MYST acetyltransferase domain in complex wit... -
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-Basic information
Entry | Database: PDB / ID: 6oir | ||||||
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Title | Crystal structure of MYST acetyltransferase domain in complex with inhibitor 62 | ||||||
Components | Histone acetyltransferase KAT8 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Inhibitor / Complex / MYST / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information MSL complex / histone H4K16 acetyltransferase activity / regulation of mRNA processing / myeloid cell differentiation / NSL complex / : / peptide-lysine-N-acetyltransferase activity / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / histone acetyltransferase complex ...MSL complex / histone H4K16 acetyltransferase activity / regulation of mRNA processing / myeloid cell differentiation / NSL complex / : / peptide-lysine-N-acetyltransferase activity / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / histone acetyltransferase complex / histone acetyltransferase / transcription initiation-coupled chromatin remodeling / neurogenesis / regulation of autophagy / transcription coregulator activity / kinetochore / nuclear matrix / HATs acetylate histones / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å | ||||||
Authors | Hermans, S.J. / Chung, M.C. / Parker, M.W. / Thomas, T. / Baell, J.B. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2019 Title: Discovery of Benzoylsulfonohydrazides as Potent Inhibitors of the Histone Acetyltransferase KAT6A. Authors: Leaver, D.J. / Cleary, B. / Nguyen, N. / Priebbenow, D.L. / Lagiakos, H.R. / Sanchez, J. / Xue, L. / Huang, F. / Sun, Y. / Mujumdar, P. / Mudududdla, R. / Varghese, S. / Teguh, S. / Charman, ...Authors: Leaver, D.J. / Cleary, B. / Nguyen, N. / Priebbenow, D.L. / Lagiakos, H.R. / Sanchez, J. / Xue, L. / Huang, F. / Sun, Y. / Mujumdar, P. / Mudududdla, R. / Varghese, S. / Teguh, S. / Charman, S.A. / White, K.L. / Katneni, K. / Cuellar, M. / Strasser, J.M. / Dahlin, J.L. / Walters, M.A. / Street, I.P. / Monahan, B.J. / Jarman, K.E. / Sabroux, H.J. / Falk, H. / Chung, M.C. / Hermans, S.J. / Parker, M.W. / Thomas, T. / Baell, J.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6oir.cif.gz | 71.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oir.ent.gz | 55 KB | Display | PDB format |
PDBx/mmJSON format | 6oir.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/6oir ftp://data.pdbj.org/pub/pdb/validation_reports/oi/6oir | 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: 32140.057 Da / Num. of mol.: 1 / Fragment: residues 176-448 / Mutation: A142S, L145M, T146I, K157R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KAT8, MOF, MYST1, PP7073 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H7Z6, histone acetyltransferase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-MNJ / |
#4: Chemical | ChemComp-GOL / |
#5: 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: 2.52 Å3/Da / Density % sol: 51.2 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% PEG 3350, 2% Tacsimate pH 7.0, 0.1 M HEPES pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 8, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→43.48 Å / Num. obs: 21626 / % possible obs: 99.95 % / Redundancy: 7.2 % / Rpim(I) all: 0.037 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.03→2.103 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 5 / Num. unique obs: 2120 / Rpim(I) all: 0.168 / % possible all: 99.72 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→43.48 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.891 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.156 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 25.191 Å2
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Refinement step | Cycle: 1 / Resolution: 2.03→43.48 Å
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