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Yorodumi- PDB-6r3d: Crystal structure of di-phosphorylated human CLK1 in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r3d | ||||||
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Title | Crystal structure of di-phosphorylated human CLK1 in complex with 4-(6,7-dichloro-1H-indol-3-yl)pyrimidin-2-amine | ||||||
Components | Dual specificity protein kinase CLK1 | ||||||
Keywords | SIGNALING PROTEIN / splicing / kinase / viral infection | ||||||
Function / homology | Function and homology information dual-specificity kinase / regulation of RNA splicing / protein serine/threonine/tyrosine kinase activity / non-membrane spanning protein tyrosine kinase activity / protein tyrosine kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Livnah, O. / Domovich, Y. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of di-phosphorylated human CLK1 in complex with 4-(1-methyl-1H-indol-3-yl)pyrimidin-2-amine Authors: Livnah, O. / Domovich, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r3d.cif.gz | 84.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r3d.ent.gz | 62.4 KB | Display | PDB format |
PDBx/mmJSON format | 6r3d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r3/6r3d ftp://data.pdbj.org/pub/pdb/validation_reports/r3/6r3d | HTTPS FTP |
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-Related structure data
Related structure data | 2vagS S: Starting model for refinement |
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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
#1: Protein | Mass: 39449.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CLK1, CLK / Production host: Escherichia coli (E. coli) / References: UniProt: P49759, dual-specificity kinase |
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#2: Chemical | ChemComp-JQW / |
#3: 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: 2.46 Å3/Da / Density % sol: 49.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 24% PEG 3350, 200mM MgCl2, 100mM BisTris (pH 6.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→47.52 Å / Num. obs: 35238 / % possible obs: 99.8 % / Redundancy: 6.2 % / Rsym value: 0.051 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.85→1.898 Å / Num. unique obs: 2095 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VAG Resolution: 1.85→47.52 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.901 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.145 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.963 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→47.52 Å
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Refine LS restraints |
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