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- PDB-6pdc: Crystal structure of MYST acetyltransferase domain in complex wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6pdc | ||||||
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Title | Crystal structure of MYST acetyltransferase domain in complex with inhibitor 42 | ||||||
![]() | Histone acetyltransferase KAT8 | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / Inhibitor / Complex / MYST / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | ![]() positive regulation of skeletal muscle satellite cell differentiation / regulation of mitochondrial transcription / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / MSL complex / histone H4K16 acetyltransferase activity / protein propionyltransferase activity / regulation of mRNA processing / histone H4 acetyltransferase activity / myeloid cell differentiation ...positive regulation of skeletal muscle satellite cell differentiation / regulation of mitochondrial transcription / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / MSL complex / histone H4K16 acetyltransferase activity / protein propionyltransferase activity / regulation of mRNA processing / histone H4 acetyltransferase activity / myeloid cell differentiation / post-embryonic hemopoiesis / negative regulation of epithelial to mesenchymal transition / NSL complex / peptide-lysine-N-acetyltransferase activity / negative regulation of type I interferon production / oogenesis / NuA4 histone acetyltransferase complex / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / histone acetyltransferase complex / positive regulation of transcription initiation by RNA polymerase II / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / transcription initiation-coupled chromatin remodeling / neurogenesis / regulation of autophagy / transcription coregulator activity / kinetochore / nuclear matrix / chromosome / HATs acetylate histones / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / negative regulation of DNA-templated transcription / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / mitochondrion / nucleoplasm / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hermans, S.J. / Parker, M.W. / Thomas, T. / Baell, J.B. | ||||||
![]() | ![]() Title: Discovery of Acylsulfonohydrazide-Derived Inhibitors of the Lysine Acetyltransferase, KAT6A, as Potent Senescence-Inducing Anti-Cancer Agents. Authors: Priebbenow, D.L. / Leaver, D.J. / Nguyen, N. / Cleary, B. / Lagiakos, H.R. / Sanchez, J. / Xue, L. / Huang, F. / Sun, Y. / Mujumdar, P. / Mudududdla, R. / Varghese, S. / Teguh, S. / Charman, ...Authors: Priebbenow, D.L. / Leaver, D.J. / Nguyen, N. / Cleary, B. / 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. / Shackleford, D.M. / Katneni, K. / Cuellar, M. / Strasser, J.M. / Dahlin, J.L. / Walters, M.A. / Street, I.P. / Monahan, B.J. / Jarman, K.E. / Jousset Sabroux, H. / Falk, H. / Chung, M.C. / Hermans, S.J. / Downer, N.L. / Parker, M.W. / Voss, A.K. / Thomas, T. / Baell, J.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.6 KB | Display | ![]() |
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PDB format | ![]() | 55.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6owhC ![]() 6owiC ![]() 6pd8C ![]() 6pd9C ![]() 6pdaC ![]() 6pdbC ![]() 6pddC ![]() 6pdeC ![]() 6pdfC ![]() 6pdgC ![]() 6ba2S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 31941.795 Da / Num. of mol.: 1 / Mutation: A142S, L145M, T146I, K157R, W204S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 195 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/O9P.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/O9P.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | ChemComp-NA / | ||||||
#4: Chemical | #5: Chemical | ChemComp-SO4 / | #6: Chemical | ChemComp-O9P / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.19 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 27% PEG 3350, 0.2 M ammonium sulfate, 0.1 M bis-tris pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 29, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→41.689 Å / Num. obs: 22986 / % possible obs: 96.1 % / Redundancy: 6.2 % / Rpim(I) all: 0.039 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.96→2.03 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2294 / Rpim(I) all: 0.336 / % possible all: 96.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6BA2 Resolution: 1.96→41.689 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.83
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.96→41.689 Å
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Refine LS restraints |
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LS refinement shell |
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