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Yorodumi- PDB-6pzs: Crystal structure of Danio rerio histone deacetylase 6 catalytic ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pzs | ||||||
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Title | Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with JR005 | ||||||
Components | Hdac6 protein | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Histone deacetylase / metallohydrolase / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information : / Aggrephagy / : / tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / histone deacetylase activity / regulation of tubulin deacetylation / potassium ion binding ...: / Aggrephagy / : / tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / histone deacetylase activity / regulation of tubulin deacetylation / 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 | Danio rerio (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å | ||||||
Authors | Osko, J.D. / Christianson, D.W. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Med.Chem. / Year: 2020 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pzs.cif.gz | 97.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pzs.ent.gz | 70.2 KB | Display | PDB format |
PDBx/mmJSON format | 6pzs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/6pzs ftp://data.pdbj.org/pub/pdb/validation_reports/pz/6pzs | HTTPS FTP |
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-Related structure data
Related structure data | 6pzoC 6pzrC 6pzuC 6q0zC 5eemS 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39724.973 Da / Num. of mol.: 1 / Fragment: catalytic domain 2 (UNP residues 290-646) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: hdac6 / Production host: Escherichia coli (E. coli) References: UniProt: A7YT55, UniProt: F8W4B7*PLUS, histone deacetylase |
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-Non-polymers , 6 types, 407 molecules
#2: Chemical | ChemComp-ZN / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-P7J / | #5: Chemical | ChemComp-CL / | #6: Chemical | #7: 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: 2.61 Å3/Da / Density % sol: 52.86 % / Description: thick plate-like crystals |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 10 mg/mL zCD2 protein, 2 mM JR005 inhibitor, 0.2 lithium nitrate, 20% w/v PEG3350, 1:1 ratio protein to precipitant |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2018 |
Radiation | Monochromator: 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: 1.79→47.39 Å / Num. obs: 39180 / % possible obs: 99.5 % / Redundancy: 6.1 % / CC1/2: 0.958 / Rmerge(I) obs: 0.282 / Rpim(I) all: 0.123 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 1.79→1.85 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.101 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3857 / CC1/2: 0.504 / Rpim(I) all: 0.527 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 5EEM Resolution: 1.79→47.39 Å / Cross valid method: FREE R-VALUE /
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Refinement step | Cycle: LAST / Resolution: 1.79→47.39 Å
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