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Yorodumi- PDB-6fyr: X-RAY STRUCTURE OF CLK3-KD(GP-[275-632], NON-PHOS.)/Cpd-2 AT 1.42A -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fyr | ||||||
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Title | X-RAY STRUCTURE OF CLK3-KD(GP-[275-632], NON-PHOS.)/Cpd-2 AT 1.42A | ||||||
Components | Dual specificity protein kinase CLK3 | ||||||
Keywords | TRANSFERASE / SPLICING / KINASE / TYROSINE-PROTEIN KINASE / SERINE/ THREONINE- PROTEIN KINASE / NUCLEOTIDE-BINDING | ||||||
Function / homology | Function and homology information dual-specificity kinase / intermediate filament cytoskeleton / regulation of RNA splicing / protein serine/threonine/tyrosine kinase activity / acrosomal vesicle / protein tyrosine kinase activity / nuclear speck / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity ...dual-specificity kinase / intermediate filament cytoskeleton / regulation of RNA splicing / protein serine/threonine/tyrosine kinase activity / acrosomal vesicle / protein tyrosine kinase activity / nuclear speck / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / RNA binding / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.42 Å | ||||||
Authors | Kallen, J. | ||||||
Citation | Journal: ChemMedChem / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fyr.cif.gz | 180.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fyr.ent.gz | 139.9 KB | Display | PDB format |
PDBx/mmJSON format | 6fyr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fyr_validation.pdf.gz | 660 KB | Display | wwPDB validaton report |
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Full document | 6fyr_full_validation.pdf.gz | 662.3 KB | Display | |
Data in XML | 6fyr_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 6fyr_validation.cif.gz | 32.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/6fyr ftp://data.pdbj.org/pub/pdb/validation_reports/fy/6fyr | HTTPS FTP |
-Related structure data
Related structure data | 6fyiC 6fykC 6fylC 6fyoC 6fypSC 6fyvC C: citing same article (ref.) 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
#1: Protein | Mass: 42254.305 Da / Num. of mol.: 1 / Fragment: kinase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CLK3 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P49761, dual-specificity kinase |
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#2: Chemical | ChemComp-EAQ / |
#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: 2.2 Å3/Da / Density % sol: 44.04 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% PEG4000, 0.1M HEPES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00003 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2016 |
Radiation | Monochromator: SI 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→19.52 Å / Num. obs: 68259 / % possible obs: 98 % / Redundancy: 3.4 % / Biso Wilson estimate: 20.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.058 / Net I/σ(I): 14.2 / Num. measured all: 230080 |
Reflection shell | Resolution: 1.42→1.46 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 2.7 / CC1/2: 0.82 / Rrim(I) all: 0.537 / % possible all: 96.2 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6FYP Resolution: 1.42→19.52 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.993 / SU ML: 0.036 / SU R Cruickshank DPI: 0.0846 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.065 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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: 61.26 Å2 / Biso mean: 16.848 Å2 / Biso min: 6.49 Å2
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Refinement step | Cycle: final / Resolution: 1.42→19.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.42→1.457 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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