+Open data
-Basic information
Entry | Database: PDB / ID: 5dn3 | |||||||||
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Title | Aurora A in complex with ATP and AA35. | |||||||||
Components | Aurora kinase A | |||||||||
Keywords | TRANSFERASE / Aurora A kinase / mitotic kinase / PPI | |||||||||
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 / 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | |||||||||
Authors | Janecek, M. / Rossmann, M. / Sharma, P. / Emery, A. / McKenzie, G. / Huggins, D. / Stockwell, S. / Stokes, J.A. / Almeida, E.G. / Hardwick, B. ...Janecek, M. / Rossmann, M. / Sharma, P. / Emery, A. / McKenzie, G. / Huggins, D. / Stockwell, S. / Stokes, J.A. / Almeida, E.G. / Hardwick, B. / Narvaez, A.J. / Hyvonen, M. / Spring, D.R. / Venkitaraman, A. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Sci Rep / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dn3.cif.gz | 77.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dn3.ent.gz | 55.1 KB | Display | PDB format |
PDBx/mmJSON format | 5dn3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dn3_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5dn3_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5dn3_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 5dn3_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/5dn3 ftp://data.pdbj.org/pub/pdb/validation_reports/dn/5dn3 | HTTPS FTP |
-Related structure data
Related structure data | 5dnrC 5dosC 5dpvC 5dr2C 5dr6C 5dr9C 5drdC 5dt0C 5dt3C 5dt4C 3fdnS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 31536.131 Da / Num. of mol.: 1 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) / Strain (production host): BL21(DE3) / Variant (production host): pUBS5120 References: UniProt: O14965, non-specific serine/threonine protein kinase |
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-Non-polymers , 5 types, 151 molecules
#2: Chemical | ChemComp-MG / |
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#3: Chemical | ChemComp-5DN / |
#4: Chemical | ChemComp-SO4 / |
#5: Chemical | ChemComp-ATP / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.62 Å3/Da / Density % sol: 66 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 50 mM HEPES, 200 mM magnesium sulfate, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 13, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→68.46 Å / Num. obs: 29802 / % possible obs: 99.9 % / Redundancy: 9.8 % / Biso Wilson estimate: 41.39 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 27.7 |
Reflection shell | Resolution: 2.05→2.1 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 3.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3FDN Resolution: 2.05→25.91 Å / Cor.coef. Fo:Fc: 0.9491 / Cor.coef. Fo:Fc free: 0.9505 / SU R Cruickshank DPI: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.14 / SU Rfree Blow DPI: 0.12 / SU Rfree Cruickshank DPI: 0.118
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Displacement parameters | Biso mean: 45.62 Å2
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Refine analyze | Luzzati coordinate error obs: 0.239 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.05→25.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.12 Å / Total num. of bins used: 15
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