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Open data
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Basic information
Entry | Database: PDB / ID: 6fyk | ||||||
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Title | X-Ray structure of CLK2-KD(136-496)/Indazole1 at 2.39A | ||||||
![]() | Dual specificity protein kinase CLK2 | ||||||
![]() | TRANSFERASE / SPLICING / PHOSPHOTRANSFERASE | ||||||
Function / homology | ![]() dual-specificity kinase / response to ionizing radiation / regulation of RNA splicing / negative regulation of gluconeogenesis / protein serine/threonine/tyrosine kinase activity / protein tyrosine kinase activity / protein autophosphorylation / nuclear body / nuclear speck / protein phosphorylation ...dual-specificity kinase / response to ionizing radiation / regulation of RNA splicing / negative regulation of gluconeogenesis / protein serine/threonine/tyrosine kinase activity / protein tyrosine kinase activity / protein autophosphorylation / nuclear body / nuclear speck / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / nucleoplasm / ATP binding / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kallen, J. | ||||||
![]() | ![]() Title: X-ray Structures and Feasibility Assessment of CLK2 Inhibitors for Phelan-McDermid Syndrome. Authors: Kallen, J. / Bergsdorf, C. / Arnaud, B. / Bernhard, M. / Brichet, M. / Cobos-Correa, A. / Elhajouji, A. / Freuler, F. / Galimberti, I. / Guibourdenche, C. / Haenni, S. / Holzinger, S. / ...Authors: Kallen, J. / Bergsdorf, C. / Arnaud, B. / Bernhard, M. / Brichet, M. / Cobos-Correa, A. / Elhajouji, A. / Freuler, F. / Galimberti, I. / Guibourdenche, C. / Haenni, S. / Holzinger, S. / Hunziker, J. / Izaac, A. / Kaufmann, M. / Leder, L. / Martus, H.J. / von Matt, P. / Polyakov, V. / Roethlisberger, P. / Roma, G. / Stiefl, N. / Uteng, M. / Lerchner, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 234.5 KB | Display | ![]() |
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PDB format | ![]() | 187.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6fyiSC ![]() 6fylC ![]() 6fyoC ![]() 6fypC ![]() 6fyrC ![]() 6fyvC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 42767.500 Da / Num. of mol.: 3 / Fragment: kinase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.29 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20% PEG2000, 0.2M trimethylamine n-oxide, 0.1M TRIS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2016 |
Radiation | Monochromator: SI 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99986 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→19.68 Å / Num. obs: 47518 / % possible obs: 99.8 % / Redundancy: 10 % / Biso Wilson estimate: 37.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.163 / Rrim(I) all: 0.171 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.39→2.45 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.927 / Mean I/σ(I) obs: 2.9 / CC1/2: 0.859 / Rrim(I) all: 0.981 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6FYI Resolution: 2.39→19.68 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.923 / SU B: 7.441 / SU ML: 0.171 / SU R Cruickshank DPI: 0.5139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.514 / ESU R Free: 0.252 Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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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 max: 155.99 Å2 / Biso mean: 36.307 Å2 / Biso min: 14.79 Å2
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Refinement step | Cycle: final / Resolution: 2.39→19.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.39→2.451 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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