+Open data
-Basic information
Entry | Database: PDB / ID: 5x8i | ||||||
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Title | Crystal structure of human CLK1 in complex with compound 25 | ||||||
Components | Dual specificity protein kinase CLK1 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Inhibitor / Complex / Kinase / CLK1 / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
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: 1.902 Å | ||||||
Authors | Sun, Q.Z. / Lin, G.F. / Li, L.L. / Jin, X.T. / Huang, L.Y. / Zhang, G. / Wei, Y.Q. / Lu, G.W. / Yang, S.Y. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2017 Title: Discovery of Potent and Selective Inhibitors of Cdc2-Like Kinase 1 (CLK1) as a New Class of Autophagy Inducers Authors: Sun, Q.Z. / Lin, G.F. / Li, L.L. / Jin, X.T. / Huang, L.Y. / Zhang, G. / Yang, W. / Chen, K. / Xiang, R. / Chen, C. / Wei, Y.Q. / Lu, G.W. / Yang, S.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5x8i.cif.gz | 295.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x8i.ent.gz | 236.9 KB | Display | PDB format |
PDBx/mmJSON format | 5x8i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x8/5x8i ftp://data.pdbj.org/pub/pdb/validation_reports/x8/5x8i | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 40565.570 Da / Num. of mol.: 2 / Fragment: UNP residues 148-484 / Mutation: R432A 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 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.17 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 2% (v/v) PEG 200, 20% (v/v) tacsimate (pH 7.0), 0.1M HEPES (pH 9.0) |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: 100 |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97849 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 8, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97849 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 58842 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 15.9 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 30.72 |
Reflection shell | Resolution: 1.9→1.97 Å / % possible obs: 100 % / Redundancy: 15.9 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 8.07 / Num. unique all: 5864 / CC1/2: 0.994 / Rsym value: 0.431 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VAG Resolution: 1.902→33.6 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.8 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.902→33.6 Å
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Refine LS restraints |
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LS refinement shell |
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