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Yorodumi- PDB-4bi1: Scaffold Focused Virtual Screening: Prospective Application to th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bi1 | ||||||
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Title | Scaffold Focused Virtual Screening: Prospective Application to the Discovery of TTK Inhibitor | ||||||
Components | DUAL SPECIFICITY PROTEIN KINASE TTK | ||||||
Keywords | TRANSFERASE / PROTEIN KINASE / MITOSIS | ||||||
Function / homology | Function and homology information protein localization to meiotic spindle midzone / meiotic spindle assembly checkpoint signaling / kinetochore binding / female meiosis chromosome segregation / protein localization to kinetochore / dual-specificity kinase / spindle organization / mitotic spindle assembly checkpoint signaling / protein serine/threonine/tyrosine kinase activity / mitotic spindle organization ...protein localization to meiotic spindle midzone / meiotic spindle assembly checkpoint signaling / kinetochore binding / female meiosis chromosome segregation / protein localization to kinetochore / dual-specificity kinase / spindle organization / mitotic spindle assembly checkpoint signaling / protein serine/threonine/tyrosine kinase activity / mitotic spindle organization / chromosome segregation / kinetochore / spindle / protein tyrosine kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / ATP binding / identical protein binding / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Langdon, S.R. / Westwood, I.M. / van Montfort, R.L.M. / Brown, N. / Blagg, J. | ||||||
Citation | Journal: J.Chem.Inf.Model / Year: 2013 Title: Scaffold-Focused Virtual Screening: Prospective Application to the Discovery of Ttk Inhibitors. Authors: Langdon, S.R. / Westwood, I.M. / Van Montfort, R.L.M. / Brown, N. / Blagg, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bi1.cif.gz | 119.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bi1.ent.gz | 90.7 KB | Display | PDB format |
PDBx/mmJSON format | 4bi1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/4bi1 ftp://data.pdbj.org/pub/pdb/validation_reports/bi/4bi1 | HTTPS FTP |
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-Related structure data
Related structure data | 4bhzC 4bi0C 4bi2C 2zmcS C: citing same article (ref.) 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: 36115.258 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 519-808 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): AI / References: UniProt: P33981, dual-specificity kinase | ||||||||
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#2: Chemical | ChemComp-7PE / #3: Chemical | ChemComp-ZO6 / | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE INCLUDING HEXAHISTID | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.67 % / Description: NONE |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 30-45% (V/V) PEG300, SITTING DROP VAPOUR DIFFUSION, 291K, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 13, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→56.78 Å / Num. obs: 12760 / % possible obs: 100 % / Observed criterion σ(I): 1.5 / Redundancy: 4 % / Biso Wilson estimate: 88.23 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZMC Resolution: 2.7→56.78 Å / Cor.coef. Fo:Fc: 0.9413 / Cor.coef. Fo:Fc free: 0.9187 / SU R Cruickshank DPI: 0.346 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.343 / SU Rfree Blow DPI: 0.245 / SU Rfree Cruickshank DPI: 0.248 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
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Displacement parameters | Biso mean: 71.83 Å2
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Refine analyze | Luzzati coordinate error obs: 0.341 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→56.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.96 Å / Total num. of bins used: 6
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Refinement TLS params. | Method: refined / Origin x: 5.0498 Å / Origin y: 32.5965 Å / Origin z: 16.9897 Å
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Refinement TLS group | Selection details: CHAIN A |