[English] 日本語
Yorodumi- PDB-8qh9: X-ray structure of Danio rerio histone deacetylase 6 (HDAC6) CD2 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qh9 | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray structure of Danio rerio histone deacetylase 6 (HDAC6) CD2 in complex with a S-29b | ||||||
Components | Histone deacetylase 6 | ||||||
Keywords | HYDROLASE / protein deacetylase / histone deacetylase 6 / zinc binding group / Inhibitor / Danio rerio | ||||||
Function / homology | Function and homology information 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 / epigenetic regulation of gene expression / angiogenesis / zinc ion binding Similarity search - Function | ||||||
Biological species | Danio rerio (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.59 Å | ||||||
Authors | Barinka, C. / Motlova, L. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Eur.J.Med.Chem. / Year: 2024 Title: Biological and structural investigation of tetrahydro-beta-carboline-based selective HDAC6 inhibitors with improved stability. Authors: Scheuerer, S. / Motlova, L. / Schaker-Hubner, L. / Sellmer, A. / Feller, F. / Ertl, F.J. / Koch, P. / Hansen, F.K. / Barinka, C. / Mahboobi, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8qh9.cif.gz | 97.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8qh9.ent.gz | 70.6 KB | Display | PDB format |
PDBx/mmJSON format | 8qh9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qh9_validation.pdf.gz | 828.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8qh9_full_validation.pdf.gz | 829.2 KB | Display | |
Data in XML | 8qh9_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 8qh9_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qh/8qh9 ftp://data.pdbj.org/pub/pdb/validation_reports/qh/8qh9 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39899.125 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: hdac6 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: F8W4B7 |
---|
-Non-polymers , 7 types, 339 molecules
#2: Chemical | ChemComp-ZN / | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
#3: Chemical | #4: Chemical | ChemComp-V9F / | Mass: 547.602 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H33N5O6 / Feature type: SUBJECT OF INVESTIGATION #5: Chemical | #6: Chemical | ChemComp-EDO / | #7: Chemical | ChemComp-PEG / | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.22 % |
---|---|
Crystal grow | Temperature: 282 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 16 % (v/v) PEG 3350 0.2 M KSCN 0.1 M Bis-Tris pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 20, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→50 Å / Num. obs: 56166 / % possible obs: 99.7 % / Redundancy: 13.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.0327 / Rrim(I) all: 0.034 / Net I/σ(I): 10.35 |
Reflection shell | Resolution: 1.59→1.68 Å / Redundancy: 13.5 % / Num. unique obs: 8875 / CC1/2: 0.45 / % possible all: 98.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.59→47.13 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.595 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.801 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.59→47.13 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|