[English] 日本語
![](img/lk-miru.gif)
- PDB-6pzr: Crystal structure of Danio rerio histone deacetylase 6 catalytic ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6pzr | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with Resminostat | ||||||
![]() | Hdac6 protein | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / Histone deacetylase / metallohydrolase / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() Aggrephagy / tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / regulation of tubulin deacetylation / histone deacetylase activity / potassium ion binding / histone deacetylase complex / hematopoietic progenitor cell differentiation ...Aggrephagy / tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / regulation of tubulin deacetylation / histone deacetylase activity / potassium ion binding / histone deacetylase complex / hematopoietic progenitor cell differentiation / angiogenesis / negative regulation of transcription by RNA polymerase II / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Osko, J.D. / Christianson, D.W. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Exploring Structural Determinants of Inhibitor Affinity and Selectivity in Complexes with Histone Deacetylase 6. Authors: Osko, J.D. / Porter, N.J. / Narayana Reddy, P.A. / Xiao, Y.C. / Rokka, J. / Jung, M. / Hooker, J.M. / Salvino, J.M. / Christianson, D.W. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 156.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 120.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 379.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 382.6 KB | Display | |
Data in XML | ![]() | 2.5 KB | Display | |
Data in CIF | ![]() | 10.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6pzoC ![]() 6pzsC ![]() 6pzuC ![]() 6q0zC ![]() 5eemS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 39812.051 Da / Num. of mol.: 2 / Fragment: catalytic domain 2 (UNP residues 289-646) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A7YT55, UniProt: F8W4B7*PLUS, histone deacetylase |
---|
-Non-polymers , 6 types, 178 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/P7D.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K.gif)
![](data/chem/img/P7D.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-K / #4: Chemical | #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-IOD / #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.8 % / Description: thick plate-like crystals |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 10 mg/mL zCD2 protein, 2 mM Resminostat inhibitor, 0.2 M potassium iodide, 20% w/v PEG3350, 1:1 ratio protein to precipitant |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 1, 2018 |
Radiation | Monochromator: Cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→68.94 Å / Num. obs: 32376 / % possible obs: 98.6 % / Redundancy: 6.4 % / CC1/2: 0.977 / Rmerge(I) obs: 0.361 / Rpim(I) all: 0.154 / Net I/σ(I): 3.4 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 1.298 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3216 / CC1/2: 0.755 / Rpim(I) all: 0.547 |
-
Processing
Software |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB Entry 5EEM Resolution: 2.3→68.94 Å / Cross valid method: FREE R-VALUE /
| ||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→68.94 Å
|