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Yorodumi- PDB-7u69: Crystal Structure of Danio rerio Histone Deacetylase 10 in Comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7u69 | ||||||
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Title | Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with Phenethyl Piperidine-4-acrylhydroxamic Acid Inhibitor | ||||||
Components | Polyamine deacetylase HDAC10 | ||||||
Keywords | HYDROLASE/INHIBITOR / Histone Deacetylase / HYDROLASE-HYDROLASE INHIBITOR complex / HYDROLASE / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information polyamine deacetylation / spermidine deacetylation / HDACs deacetylate histones / acetylspermidine deacetylase / acetylspermidine deacetylase activity / acetylputrescine deacetylase / acetylputrescine deacetylase activity / deacetylase activity / homologous recombination / swimming behavior ...polyamine deacetylation / spermidine deacetylation / HDACs deacetylate histones / acetylspermidine deacetylase / acetylspermidine deacetylase activity / acetylputrescine deacetylase / acetylputrescine deacetylase activity / deacetylase activity / homologous recombination / swimming behavior / regulation of tubulin deacetylation / macroautophagy / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Danio rerio (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Herbst-Gervasoni, C.J. / Christianson, D.W. | ||||||
Funding support | United States, 1items
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Citation | Journal: Eur.J.Med.Chem. / Year: 2022 Title: Identification of histone deacetylase 10 (HDAC10) inhibitors that modulate autophagy in transformed cells. Authors: Zeyen, P. / Zeyn, Y. / Herp, D. / Mahmoudi, F. / Yesiloglu, T.Z. / Erdmann, F. / Schmidt, M. / Robaa, D. / Romier, C. / Ridinger, J. / Herbst-Gervasoni, C.J. / Christianson, D.W. / Oehme, I. ...Authors: Zeyen, P. / Zeyn, Y. / Herp, D. / Mahmoudi, F. / Yesiloglu, T.Z. / Erdmann, F. / Schmidt, M. / Robaa, D. / Romier, C. / Ridinger, J. / Herbst-Gervasoni, C.J. / Christianson, D.W. / Oehme, I. / Jung, M. / Kramer, O.H. / Sippl, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7u69.cif.gz | 169.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7u69.ent.gz | 103.9 KB | Display | PDB format |
PDBx/mmJSON format | 7u69.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7u69_validation.pdf.gz | 655.4 KB | Display | wwPDB validaton report |
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Full document | 7u69_full_validation.pdf.gz | 658.6 KB | Display | |
Data in XML | 7u69_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | 7u69_validation.cif.gz | 34.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u6/7u69 ftp://data.pdbj.org/pub/pdb/validation_reports/u6/7u69 | HTTPS FTP |
-Related structure data
Related structure data | 7u3mC 7u6aC 7u6bC 5td7S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 75055.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: hdac10 / Production host: Escherichia coli (E. coli) References: UniProt: F1QCV2, acetylspermidine deacetylase, acetylputrescine deacetylase |
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-Non-polymers , 5 types, 120 molecules
#2: Chemical | ChemComp-LS6 / ( | ||||||
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#3: Chemical | #4: Chemical | ChemComp-ZN / | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 3.08 Å3/Da / Density % sol: 60.01 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 10 mg/mL HDAC10, 2 mM inhibitor, 1:1000 trypsin:HDAC10, 0.1 M Sodium Phosphate Monobasic, 0.1 M Sodium Phosphate Dibasic, and 20% PEG 3350. Microseed crystals of HDAC10-Tubastatin were also added to the drop |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→69.68 Å / Num. obs: 31956 / % possible obs: 97.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 42.42 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.091 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.726 / Mean I/σ(I) obs: 2 / Num. unique obs: 3211 / CC1/2: 0.594 / Rpim(I) all: 0.584 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5td7 Resolution: 2.5→69.68 Å / SU ML: 0.3271 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.7104 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.97 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→69.68 Å
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Refine LS restraints |
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LS refinement shell |
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