+Open data
-Basic information
Entry | Database: PDB / ID: 3qbn | ||||||
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Title | Structure of Human Aurora A in Complex with a diaminopyrimidine | ||||||
Components | Serine/threonine-protein kinase 6Serine/threonine-specific protein kinase | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Kinase Domain / Diaminopyrimidine / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
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 / spindle pole centrosome / positive regulation of oocyte maturation / 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 / spindle pole centrosome / positive regulation of oocyte maturation / histone H3S10 kinase activity / chromosome passenger complex / pronucleus / meiotic spindle / mitotic centrosome separation / germinal vesicle / protein localization to centrosome / anterior/posterior axis specification / centrosome localization / neuron projection extension / positive regulation of mitochondrial fission / spindle organization / mitotic spindle pole / SUMOylation of DNA replication proteins / spindle midzone / regulation of G2/M transition of mitotic cell cycle / centriole / protein serine/threonine/tyrosine kinase activity / positive regulation of mitotic cell cycle / AURKA Activation by TPX2 / mitotic spindle organization / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of mitotic nuclear division / ciliary basal body / negative regulation of protein binding / regulation of cytokinesis / regulation of signal transduction by p53 class mediator / molecular function activator activity / liver regeneration / 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 / spindle / kinetochore / response to wounding / microtubule cytoskeleton / G2/M transition of mitotic cell cycle / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / midbody / proteasome-mediated ubiquitin-dependent protein catabolic process / basolateral plasma membrane / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / microtubule / postsynaptic density / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein heterodimerization activity / cell division / negative regulation of gene expression / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / glutamatergic synapse / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / nucleoplasm / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å | ||||||
Authors | Gruetter, C. / Simard, J.R. / Rauh, D. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2011 Title: Identification of Ustilago maydis Aurora kinase as a novel antifungal target. Authors: Tueckmantel, S. / Greul, J.N. / Janning, P. / Brockmeyer, A. / Gruetter, C. / Simard, J.R. / Gutbrod, O. / Beck, M.E. / Tietjen, K. / Rauh, D. / Schreier, P.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qbn.cif.gz | 66 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qbn.ent.gz | 47.5 KB | Display | PDB format |
PDBx/mmJSON format | 3qbn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/3qbn ftp://data.pdbj.org/pub/pdb/validation_reports/qb/3qbn | HTTPS FTP |
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-Related structure data
Related structure data | 2dwbS 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: 32502.205 Da / Num. of mol.: 1 / Fragment: unp residues 124-403 / Mutation: V279C, C290S, C393S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AURKA, AIK, ARK1, AURA, BTAK, STK15, STK6 / Plasmid: pET 28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O14965, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-E9Z / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 100 mM Na-citrate, 15-20% PEG8000, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9786 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2010 / Details: Dynamic bendable mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.5→45 Å / Num. all: 4902 / Num. obs: 4883 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 112.241 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 27.27 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 39.44 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2DWB Resolution: 3.5→40 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.89 / WRfactor Rfree: 0.3115 / WRfactor Rwork: 0.2253 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6987 / SU B: 50.979 / SU ML: 0.752 / SU Rfree: 0.869 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.869 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 173.64 Å2 / Biso mean: 131.898 Å2 / Biso min: 95.68 Å2
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Refinement step | Cycle: LAST / Resolution: 3.5→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.5→3.59 Å / Total num. of bins used: 20
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