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- PDB-6g39: Crystal structure of haspin F605Y mutant in complex with 5-iodotu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6g39 | ||||||
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Title | Crystal structure of haspin F605Y mutant in complex with 5-iodotubercidin | ||||||
![]() | Serine/threonine-protein kinase haspin | ||||||
![]() | TRANSFERASE / kinase / inhibitors / slow off-rate / kinetics / halogen / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | ![]() histone H3T3 kinase activity / protein localization to chromosome, centromeric region / mitotic sister chromatid cohesion / mitotic spindle assembly checkpoint signaling / spindle / chromosome / mitotic cell cycle / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction ...histone H3T3 kinase activity / protein localization to chromosome, centromeric region / mitotic sister chromatid cohesion / mitotic spindle assembly checkpoint signaling / spindle / chromosome / mitotic cell cycle / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / centrosome / nucleoplasm / ATP binding / nucleus / cytoplasm 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 | ![]() | 160.1 KB | Display | ![]() |
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PDB format | ![]() | 124.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 801.6 KB | Display | ![]() |
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Full document | ![]() | 802.7 KB | Display | |
Data in XML | ![]() | 18 KB | Display | |
Data in CIF | ![]() | 27.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6g33C ![]() 6g34C ![]() 6g35C ![]() 6g36C ![]() 6g37C ![]() 6g38C ![]() 6g3aC ![]() 4oucS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 40727.484 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8TF76, non-specific serine/threonine protein kinase |
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-Non-polymers , 5 types, 344 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/5ID.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/5ID.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NA / | ||
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#3: Chemical | ChemComp-5ID / ( | ||
#4: Chemical | ChemComp-IOD / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.54 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 51-63% MPD and 0.1M SPG buffer, pH 6.0-6.5 / PH range: 6.0-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→22.01 Å / Num. obs: 86860 / % possible obs: 98.3 % / Redundancy: 5.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 1.45→1.53 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3 / Num. unique obs: 12366 / CC1/2: 0.801 / % possible all: 96.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4OUC Resolution: 1.45→22.01 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.838 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.051 / 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: 25.173 Å2
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Refinement step | Cycle: 1 / Resolution: 1.45→22.01 Å
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Refine LS restraints |
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