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Yorodumi- PDB-7oa0: Crystal structure of di-phosphorylated human CLK1 in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7oa0 | ||||||
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Title | Crystal structure of di-phosphorylated human CLK1 in complex with 5-(6,7-dichloro-1H-indol-3-yl)pyrimidin-4-amine | ||||||
Components | Dual specificity protein kinase CLK1 | ||||||
Keywords | SIGNALING PROTEIN / CLK1 / 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: 1.81 Å | ||||||
Authors | Livnah, O. / Domovich, Y. / Bracher, F. / Aiger, C. | ||||||
Funding support | Israel, 1items
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Citation | Journal: To Be Published Title: Development of novel CLK1 inhibitors as potential drugs for treatment of Chikungunya virus infections Authors: Livnah, O. / Domovich, Y. / Bracher, F. / Aiger, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7oa0.cif.gz | 90.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7oa0.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7oa0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7oa0_validation.pdf.gz | 760.6 KB | Display | wwPDB validaton report |
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Full document | 7oa0_full_validation.pdf.gz | 762.9 KB | Display | |
Data in XML | 7oa0_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 7oa0_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/7oa0 ftp://data.pdbj.org/pub/pdb/validation_reports/oa/7oa0 | HTTPS FTP |
-Related structure data
Related structure data | 7o9yC 6r8jS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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 BL21(DE3) (bacteria) / References: UniProt: P49759, dual-specificity kinase |
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#2: Chemical | ChemComp-JTQ / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 24% PEG3350, 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: 0.976 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→100 Å / Num. obs: 36760 / % possible obs: 99.7 % / Redundancy: 5.73 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 20.68 |
Reflection shell | Resolution: 1.81→1.87 Å / Rmerge(I) obs: 1.17 / Num. unique obs: 3320 / CC1/2: 0.679 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6R8J Resolution: 1.81→50.128 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.845 / SU ML: 0.11 / Cross valid method: FREE R-VALUE / ESU R: 0.126 / ESU R Free: 0.129 Details: Hydrogens have been added in their 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 / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.601 Å2
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Refinement step | Cycle: LAST / Resolution: 1.81→50.128 Å
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Refine LS restraints |
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LS refinement shell |
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