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- PDB-7u6a: Crystal Structure of Danio rerio Histone Deacetylase 10 in Comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7u6a | ||||||
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Title | Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with 3-thienylmethyl Benzhydroxamic Acid Inhibitor | ||||||
![]() | Polyamine deacetylase HDAC10 | ||||||
![]() | HYDROLASE/INHIBITOR / Histone Deacetylase / HYDROLASE / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Herbst-Gervasoni, C.J. / Christianson, D.W. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 172.2 KB | Display | ![]() |
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PDB format | ![]() | 105.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 716.9 KB | Display | ![]() |
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Full document | ![]() | 720.8 KB | Display | |
Data in XML | ![]() | 25 KB | Display | |
Data in CIF | ![]() | 35.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7u3mC ![]() 7u69C ![]() 7u6bC ![]() 5td7S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 75055.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: F1QCV2, acetylspermidine deacetylase, acetylputrescine deacetylase |
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-Non-polymers , 6 types, 165 molecules ![](data/chem/img/LSL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-LSL / | ||||||
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#3: Chemical | ChemComp-EDO / | ||||||
#4: Chemical | #5: Chemical | ChemComp-ZN / | #6: Chemical | #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: 3.12 Å3/Da / Density % sol: 60.59 % |
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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: ![]() ![]() ![]() |
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: 2.25→60.97 Å / Num. obs: 45730 / % possible obs: 100 % / Redundancy: 9.5 % / Biso Wilson estimate: 46.95 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.046 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.25→2.33 Å / Rmerge(I) obs: 1.266 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4484 / CC1/2: 0.69 / Rpim(I) all: 0.622 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5TD7 Resolution: 2.25→60.97 Å / SU ML: 0.2752 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.8619 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: 53.04 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→60.97 Å
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Refine LS restraints |
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LS refinement shell |
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