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Open data
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Basic information
Entry | Database: PDB / ID: 5dt3 | ||||||
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Title | Aurora A Kinase in Complex with ATP in Space Group P6122 | ||||||
![]() | Aurora kinase A | ||||||
![]() | TRANSFERASE / Aurora A kinase / mitotic kinase / PPI | ||||||
Function / homology | ![]() 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 / meiotic spindle / mitotic centrosome separation / 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 / 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 / positive regulation of mitotic nuclear division / AURKA Activation by TPX2 / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / mitotic spindle organization / ciliary basal body / regulation of cytokinesis / regulation of signal transduction by p53 class mediator / negative regulation of protein binding / 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 / spindle microtubule / mitotic spindle / kinetochore / response to wounding / spindle / G2/M transition of mitotic cell cycle / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / midbody / basolateral plasma membrane / peptidyl-serine phosphorylation / proteasome-mediated ubiquitin-dependent protein catabolic process / Regulation of TP53 Activity through Phosphorylation / protein autophosphorylation / postsynaptic density / non-specific serine/threonine protein kinase / protein kinase activity / protein heterodimerization activity / cell division / protein phosphorylation / negative regulation of gene expression / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Janecek, M. / Rossmann, M. / Sharma, P. / Emery, A. / McKenzie, G.J. / Huggins, D.J. / Stockwell, S. / Stokes, J.A. / Almeida, E.G. / Hardwick, B. ...Janecek, M. / Rossmann, M. / Sharma, P. / Emery, A. / McKenzie, G.J. / Huggins, D.J. / Stockwell, S. / Stokes, J.A. / Almeida, E.G. / Hardwick, B. / Narvaez, A.J. / Hyvonen, M. / Spring, D.R. / Venkitaraman, A.R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Allosteric modulation of AURKA kinase activity by a small-molecule inhibitor of its protein-protein interaction with TPX2. Authors: Janecek, M. / Rossmann, M. / Sharma, P. / Emery, A. / Huggins, D.J. / Stockwell, S.R. / Stokes, J.E. / Tan, Y.S. / Almeida, E.G. / Hardwick, B. / Narvaez, A.J. / Hyvonen, M. / Spring, D.R. / ...Authors: Janecek, M. / Rossmann, M. / Sharma, P. / Emery, A. / Huggins, D.J. / Stockwell, S.R. / Stokes, J.E. / Tan, Y.S. / Almeida, E.G. / Hardwick, B. / Narvaez, A.J. / Hyvonen, M. / Spring, D.R. / McKenzie, G.J. / Venkitaraman, A.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.2 KB | Display | ![]() |
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PDB format | ![]() | 52.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 776.6 KB | Display | ![]() |
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Full document | ![]() | 778.6 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 17.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5dn3C ![]() 5dnrC ![]() 5dosC ![]() 5dpvC ![]() 5dr2C ![]() 5dr6C ![]() 5dr9C ![]() 5drdC ![]() 5dt0C ![]() 5dt4C ![]() 3fdnS S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 31917.533 Da / Num. of mol.: 1 / Fragment: UNP residues 126-390 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: AURKA, AIK, AIRK1, ARK1, AURA, AYK1, BTAK, IAK1, STK15, STK6 Plasmid: pBAT4 / Details (production host): Expresses lambda phosphatase / Production host: ![]() ![]() References: UniProt: O14965, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-ATP / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.34 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 100 mM HEPES pH 7.4, 200 mM magnesium sulfate, 2-20 % PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2014 |
Radiation | Monochromator: 0.92 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.329→71.42 Å / Num. obs: 15660 / % possible obs: 100 % / Redundancy: 18.5 % / Biso Wilson estimate: 75.2 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 31 |
Reflection shell | Resolution: 2.329→2.337 Å / Redundancy: 19.6 % / Rmerge(I) obs: 1.624 / Mean I/σ(I) obs: 2.1 / Rsym value: 1.624 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3FDN Resolution: 2.33→55.07 Å / Cor.coef. Fo:Fc: 0.9416 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 0.289 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.313 / SU Rfree Blow DPI: 0.221 / SU Rfree Cruickshank DPI: 0.217
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Displacement parameters | Biso mean: 73.91 Å2
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Refine analyze | Luzzati coordinate error obs: 0.339 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.33→55.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.33→2.49 Å / Total num. of bins used: 8
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