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Yorodumi- PDB-3w2c: Structure of Aurora kinase A complexed to benzoimidazole-indazole... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3w2c | ||||||
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Title | Structure of Aurora kinase A complexed to benzoimidazole-indazole inhibitor XV | ||||||
Components | Aurora kinase A | ||||||
Keywords | TRANSFERASE / kinase / ATP competitor | ||||||
Function / homology | Function and homology information Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / positive regulation of oocyte maturation / spindle pole centrosome / histone H3S10 kinase activity / chromosome passenger complex / pronucleus ...Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / positive regulation of oocyte maturation / spindle pole centrosome / histone H3S10 kinase activity / chromosome passenger complex / pronucleus / mitotic centrosome separation / meiotic spindle / germinal vesicle / protein localization to centrosome / anterior/posterior axis specification / centrosome localization / neuron projection extension / spindle organization / positive regulation of mitochondrial fission / mitotic spindle pole / regulation of G2/M transition of mitotic cell cycle / SUMOylation of DNA replication proteins / spindle midzone / centriole / protein serine/threonine/tyrosine kinase activity / liver regeneration / AURKA Activation by TPX2 / positive regulation of mitotic nuclear division / positive regulation of mitotic cell cycle / mitotic spindle organization / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / ciliary basal body / regulation of cytokinesis / regulation of signal transduction by p53 class mediator / negative regulation of protein binding / molecular function activator activity / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / regulation of protein stability / mitotic spindle / kinetochore / G2/M transition of mitotic cell cycle / response to wounding / spindle / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / peptidyl-serine phosphorylation / basolateral plasma membrane / midbody / Regulation of TP53 Activity through Phosphorylation / proteasome-mediated ubiquitin-dependent protein catabolic process / protein autophosphorylation / microtubule / postsynaptic density / non-specific serine/threonine protein kinase / protein kinase activity / protein heterodimerization activity / protein phosphorylation / cell division / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / ubiquitin protein ligase binding / glutamatergic synapse / negative regulation of apoptotic process / protein kinase binding / apoptotic process / perinuclear region of cytoplasm / nucleoplasm / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.45 Å | ||||||
Authors | Oliveira, T.M. / Kairies, N.A. / Engh, R.A. | ||||||
Citation | Journal: To be Published Title: Flexibility and multiple conformations of the activation and glycine rich loops of aurora A accompanying inhibitor binding Authors: Oliveira, T.M. / Kairies, N. / Engh, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w2c.cif.gz | 179.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w2c.ent.gz | 142.8 KB | Display | PDB format |
PDBx/mmJSON format | 3w2c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3w2c_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3w2c_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3w2c_validation.xml.gz | 37.5 KB | Display | |
Data in CIF | 3w2c_validation.cif.gz | 48.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w2/3w2c ftp://data.pdbj.org/pub/pdb/validation_reports/w2/3w2c | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 30308.822 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 128-388 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: AURKA, AIK, AIRK1, ARK1, AURA, AYK1, BTAK, IAK1, STK15, STK6 Production host: Escherichia coli (E. coli) References: UniProt: O14965, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-N15 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.74 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.488 Å | |||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 1, 2010 | |||||||||||||||||||||||||
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 | |||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.4→45.731 Å / Num. all: 66919 / Num. obs: 50800 / % possible obs: 85 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 | |||||||||||||||||||||||||
Reflection shell | Resolution: 2.45→2.48 Å / % possible all: 49 |
-Processing
Software |
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Refinement | Resolution: 2.45→45.73 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.871 / SU B: 12.083 / SU ML: 0.283 / Cross valid method: THROUGHOUT / ESU R: 0.712 / ESU R Free: 0.371 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.84 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→45.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.514 Å / Total num. of bins used: 20
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