+Open data
-Basic information
Entry | Database: PDB / ID: 6yta | ||||||
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Title | CLK1 bound with imidazopyridazine (Cpd 1) | ||||||
Components | Dual specificity protein kinase CLK1 | ||||||
Keywords | TRANSFERASE / Inhibitor / Complex / CLK1 / 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: 2.3 Å | ||||||
Authors | Schroeder, M. / Chaikuad, A. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J.Med.Chem. / Year: 2020 Title: DFG-1 Residue Controls Inhibitor Binding Mode and Affinity, Providing a Basis for Rational Design of Kinase Inhibitor Selectivity. Authors: Schroder, M. / Bullock, A.N. / Fedorov, O. / Bracher, F. / Chaikuad, A. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yta.cif.gz | 155.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yta.ent.gz | 120.3 KB | Display | PDB format |
PDBx/mmJSON format | 6yta.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/6yta ftp://data.pdbj.org/pub/pdb/validation_reports/yt/6yta | HTTPS FTP |
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-Related structure data
Related structure data | 6ytdC 6yteC 6ytgC 6ytiC 6ytwC 6ytyC 6yu1C 6z2vC 6zlnC 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: 39581.512 Da / Num. of mol.: 1 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 |
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#2: Chemical | ChemComp-EDO / |
#3: Chemical | ChemComp-IYZ / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.66 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 14% PEG 6k, 0.1M bicine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 8, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→64.3 Å / Num. obs: 16584 / % possible obs: 99.2 % / Redundancy: 5.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.026 / Rrim(I) all: 0.061 / Net I/σ(I): 20.6 / Num. measured all: 86772 / Scaling rejects: 681 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1z57 Resolution: 2.3→64.3 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.847 / SU B: 13.205 / SU ML: 0.177 / SU R Cruickshank DPI: 0.3896 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.39 / ESU R Free: 0.281 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 66.7 Å2 / Biso mean: 21.79 Å2 / Biso min: 7.75 Å2
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Refinement step | Cycle: final / Resolution: 2.3→64.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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