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Yorodumi- PDB-6i5i: Crystal structure of CLK1 in complexed with furo[3,2-b]pyridine c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i5i | ||||||
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Title | Crystal structure of CLK1 in complexed with furo[3,2-b]pyridine compound 12h | ||||||
Components | Dual specificity protein kinase CLK1 | ||||||
Keywords | TRANSFERASE / splicing kinase / furopyridine / inhibitor / CLK / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
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: 1.6 Å | ||||||
Authors | Chaikuad, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Paruch, K. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2019 Title: Furo[3,2-b]pyridine: A Privileged Scaffold for Highly Selective Kinase Inhibitors and Effective Modulators of the Hedgehog Pathway. Authors: Nemec, V. / Hylsova, M. / Maier, L. / Flegel, J. / Sievers, S. / Ziegler, S. / Schroder, M. / Berger, B.T. / Chaikuad, A. / Valcikova, B. / Uldrijan, S. / Drapela, S. / Soucek, K. / ...Authors: Nemec, V. / Hylsova, M. / Maier, L. / Flegel, J. / Sievers, S. / Ziegler, S. / Schroder, M. / Berger, B.T. / Chaikuad, A. / Valcikova, B. / Uldrijan, S. / Drapela, S. / Soucek, K. / Waldmann, H. / Knapp, S. / Paruch, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6i5i.cif.gz | 160.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i5i.ent.gz | 125 KB | Display | PDB format |
PDBx/mmJSON format | 6i5i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/6i5i ftp://data.pdbj.org/pub/pdb/validation_reports/i5/6i5i | HTTPS FTP |
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-Related structure data
Related structure data | 6i5hC 6i5kC 6i5lC 6g33S 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: 39581.512 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CLK1, CLK / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2 / References: UniProt: P49759, dual-specificity kinase | ||
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#2: Chemical | ChemComp-H3E / | ||
#3: Chemical | ChemComp-EDO / #4: 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: 2.54 Å3/Da / Density % sol: 51.55 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 20% PEG 6000, 0.1M bicine pH 9.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.99 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 8, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→49.32 Å / Num. obs: 51989 / % possible obs: 99.4 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 3 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 7542 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6G33 Resolution: 1.6→49.32 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.559 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.081 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.596 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→49.32 Å
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Refine LS restraints |
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