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Open data
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Basic information
Entry | Database: PDB / ID: 6g33 | ||||||
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Title | Crystal structure of CLK1 in complex with 5-iodotubercidin | ||||||
![]() | (Dual specificity protein kinase ...) x 2 | ||||||
![]() | TRANSFERASE / kinase / inhibitors / slow off-rate / kinetics / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Heroven, C. / Chaikuad, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Halogen-Aromatic pi Interactions Modulate Inhibitor Residence Times. Authors: Heroven, C. / Georgi, V. / Ganotra, G.K. / Brennan, P. / Wolfreys, F. / Wade, R.C. / Fernandez-Montalvan, A.E. / Chaikuad, A. / Knapp, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 427.8 KB | Display | ![]() |
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PDB format | ![]() | 352.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 39.9 KB | Display | |
Data in CIF | ![]() | 56.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6g34C ![]() 6g35C ![]() 6g36C ![]() 6g37C ![]() 6g38C ![]() 6g39C ![]() 6g3aC ![]() 2vagS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: -1 - 482 / Label seq-ID: 1 - 337
NCS ensembles :
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Components
-Dual specificity protein kinase ... , 2 types, 3 molecules ABC
#1: Protein | Mass: 39741.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 39581.512 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 4 types, 348 molecules ![](data/chem/img/5ID.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PO4 / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.14 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% 1,2-propanediol, 5% glycerol and 0.1 M NaKPO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 5, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0282 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→29.34 Å / Num. obs: 72225 / % possible obs: 99.9 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.05→2.16 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 10553 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2vag Resolution: 2.05→89.86 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 10.983 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.162 / 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: 47.364 Å2
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Refinement step | Cycle: 1 / Resolution: 2.05→89.86 Å
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Refine LS restraints |
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