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Yorodumi- PDB-4bc6: Crystal structure of human serine threonine kinase-10 bound to no... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bc6 | |||||||||
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Title | Crystal structure of human serine threonine kinase-10 bound to novel Bosutinib Isoform 1, previously thought to be Bosutinib | |||||||||
Components | SERINE/THREONINE-PROTEIN KINASE 10Serine/threonine-specific protein kinase | |||||||||
Keywords | TRANSFERASE | |||||||||
Function / homology | Function and homology information lymphocyte aggregation / regulation of lymphocyte migration / RHOB GTPase cycle / RHOC GTPase cycle / RHOA GTPase cycle / specific granule membrane / protein autophosphorylation / non-specific serine/threonine protein kinase / cell cycle / protein phosphorylation ...lymphocyte aggregation / regulation of lymphocyte migration / RHOB GTPase cycle / RHOC GTPase cycle / RHOA GTPase cycle / specific granule membrane / protein autophosphorylation / non-specific serine/threonine protein kinase / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / Neutrophil degranulation / protein homodimerization activity / extracellular exosome / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Vollmar, M. / Szklarz, M. / Chaikuad, A. / Elkins, J. / Savitsky, P. / Azeez, K.A. / Salah, E. / Krojer, T. / Canning, P. / Muniz, J.R.C. ...Vollmar, M. / Szklarz, M. / Chaikuad, A. / Elkins, J. / Savitsky, P. / Azeez, K.A. / Salah, E. / Krojer, T. / Canning, P. / Muniz, J.R.C. / Bountra, C. / Arrowsmith, C.H. / von Delft, F. / Weigelt, J. / Edwards, A. / Knapp, S. | |||||||||
Citation | Journal: To be Published Title: Crystal Structure of Human Serine Threonine Kinase- 10 Bound to Novel Bosutinib Isoform 1, Previously Thought to be Bosutinib Authors: Vollmar, M. / Szklarz, M. / Chaikuad, A. / Elkins, J. / Savitsky, P. / Azeez, K.A. / Salah, E. / Krojer, T. / Canning, P. / Muniz, J.R.C. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / ...Authors: Vollmar, M. / Szklarz, M. / Chaikuad, A. / Elkins, J. / Savitsky, P. / Azeez, K.A. / Salah, E. / Krojer, T. / Canning, P. / Muniz, J.R.C. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / von Delft, F. / Knapp, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bc6.cif.gz | 127 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bc6.ent.gz | 97.4 KB | Display | PDB format |
PDBx/mmJSON format | 4bc6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/4bc6 ftp://data.pdbj.org/pub/pdb/validation_reports/bc/4bc6 | HTTPS FTP |
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-Related structure data
Related structure data | 2j7tS S: Starting model for refinement |
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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: 33128.289 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 24-316 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-LAMBDA-PPASE References: UniProt: O94804, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-XZN / |
#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: 2.86 Å3/Da / Density % sol: 57.04 % / Description: NONE |
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Crystal grow | Details: 0.1M SPG PH 7.0; 60% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 13, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→19.18 Å / Num. obs: 20251 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 49.61 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.9 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2J7T Resolution: 2.2→19.18 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.9047 / SU R Cruickshank DPI: 0.203 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.201 / SU Rfree Blow DPI: 0.181 / SU Rfree Cruickshank DPI: 0.183 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
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Displacement parameters | Biso mean: 93.76 Å2
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Refine analyze | Luzzati coordinate error obs: 0.506 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→19.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.32 Å / Total num. of bins used: 10
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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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