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Yorodumi- PDB-6oip: Crystal structure of MYST acetyltransferase domain in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6oip | ||||||
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Title | Crystal structure of MYST acetyltransferase domain in complex with inhibitor 34 | ||||||
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: 1.8 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 | 6oip.cif.gz | 81.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oip.ent.gz | 57.3 KB | Display | PDB format |
PDBx/mmJSON format | 6oip.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/6oip ftp://data.pdbj.org/pub/pdb/validation_reports/oi/6oip | HTTPS FTP |
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-Related structure data
Related structure data | 6oinC 6oioC 6oiqC 6oirC 2pq8S S: Starting model for refinement C: citing same article (ref.) |
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Similar 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 177-448 / 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 | #4: Chemical | ChemComp-MLS / | #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: 2.51 Å3/Da / Density % sol: 51 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% PEG 3350, 0.2 M K/Na Tartrate |
-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: Jun 10, 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: 1.8→34.313 Å / Num. obs: 30658 / % possible obs: 99.9 % / Redundancy: 6.8 % / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.8→1.864 Å / Mean I/σ(I) obs: 4 / Num. unique obs: 3054 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PQ8 Resolution: 1.8→34.313 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 19.61 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→34.313 Å
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Refine LS restraints |
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LS refinement shell |
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