+Open data
-Basic information
Entry | Database: PDB / ID: 6ytd | ||||||
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Title | CLK1 V324A mutant bound with benzothiazole Tg003 (Cpd 2) | ||||||
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 / 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 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 | 6ytd.cif.gz | 129.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ytd.ent.gz | 98.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ytd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ytd_validation.pdf.gz | 674.5 KB | Display | wwPDB validaton report |
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Full document | 6ytd_full_validation.pdf.gz | 675.3 KB | Display | |
Data in XML | 6ytd_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 6ytd_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/6ytd ftp://data.pdbj.org/pub/pdb/validation_reports/yt/6ytd | HTTPS FTP |
-Related structure data
Related structure data | 6ytaC 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: 39553.457 Da / Num. of mol.: 1 / Mutation: V324A 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-EAE / ( |
#3: 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: 2.69 Å3/Da / Density % sol: 54.19 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 17% PEG 3350, 0,2M Na malonate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 28, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2→48.56 Å / Num. obs: 27570 / % possible obs: 97.1 % / Redundancy: 6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.043 / Rrim(I) all: 0.106 / Net I/σ(I): 10.2 / Num. measured all: 165050 / Scaling rejects: 78 | ||||||||||||||||||||||||||||||
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→45.81 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.371 / SU ML: 0.112 / SU R Cruickshank DPI: 0.1719 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.16 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: 87.33 Å2 / Biso mean: 28.811 Å2 / Biso min: 15.8 Å2
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Refinement step | Cycle: final / Resolution: 2→45.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 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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