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Yorodumi- PDB-2vag: Crystal structure of di-phosphorylated human CLK1 in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vag | ||||||
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Title | Crystal structure of di-phosphorylated human CLK1 in complex with a novel substituted indole inhibitor | ||||||
Components | DUAL SPECIFICITY PROTEIN KINASE CLK1 | ||||||
Keywords | TRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / TYROSINE-PROTEIN KINASE / NUCLEUS | ||||||
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: 1.8 Å | ||||||
Authors | Pike, A.C.W. / Bullock, A.N. / Fedorov, O. / Pilka, E.S. / Ugochukwu, E. / von Delft, F. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. ...Pike, A.C.W. / Bullock, A.N. / Fedorov, O. / Pilka, E.S. / Ugochukwu, E. / von Delft, F. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Huber, K. / Bracher, F. / Knapp, S. | ||||||
Citation | Journal: Chem.Biol / Year: 2011 Title: Specific Clk Inhibitors from a Novel Chemotype for Regulation of Alternative Splicing. Authors: Fedorov, O. / Huber, K. / Eisenreich, A. / Filippakopoulos, P. / King, O. / Bullock, A.N. / Szklarczyk, D. / Jensen, L.J. / Fabbro, D. / Trappe, J. / Rauch, U. / Bracher, F. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vag.cif.gz | 88.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vag.ent.gz | 63.8 KB | Display | PDB format |
PDBx/mmJSON format | 2vag.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vag_validation.pdf.gz | 837.4 KB | Display | wwPDB validaton report |
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Full document | 2vag_full_validation.pdf.gz | 840.1 KB | Display | |
Data in XML | 2vag_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 2vag_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/va/2vag ftp://data.pdbj.org/pub/pdb/validation_reports/va/2vag | HTTPS FTP |
-Related structure data
Related structure data | 2wu6C 2wu7C 1z57S S: Starting model for refinement C: citing same article (ref.) |
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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: 39741.469 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 148-484 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PLIC-SGC1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): R3 / References: UniProt: P49759, dual-specificity kinase |
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#2: Chemical | ChemComp-V25 / |
#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: 2.57 Å3/Da / Density % sol: 52.9 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 2.1M SODIUM MALATE PH7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.006029 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 15, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.006029 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→33.58 Å / Num. obs: 36979 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 25.45 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.8 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Z57 Resolution: 1.8→32 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.058 / SU ML: 0.096 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.52 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→32 Å
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Refine LS restraints |
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