+Open data
-Basic information
Entry | Database: PDB / ID: 5ew9 | ||||||
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Title | Crystal Structure of Aurora A Kinase Domain Bound to MK-5108 | ||||||
Components | Aurora kinase A | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Transferase / Protein Kinase / Inhibitor / 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 / 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: 2.181 Å | ||||||
Authors | Shiau, A.K. / Motamedi, A. | ||||||
Citation | Journal: Front Oncol / Year: 2015 Title: A Cell Biologist's Field Guide to Aurora Kinase Inhibitors. Authors: de Groot, C.O. / Hsia, J.E. / Anzola, J.V. / Motamedi, A. / Yoon, M. / Wong, Y.L. / Jenkins, D. / Lee, H.J. / Martinez, M.B. / Davis, R.L. / Gahman, T.C. / Desai, A. / Shiau, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ew9.cif.gz | 125.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ew9.ent.gz | 94.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ew9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ew9_validation.pdf.gz | 837.8 KB | Display | wwPDB validaton report |
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Full document | 5ew9_full_validation.pdf.gz | 838.5 KB | Display | |
Data in XML | 5ew9_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 5ew9_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ew/5ew9 ftp://data.pdbj.org/pub/pdb/validation_reports/ew/5ew9 | HTTPS FTP |
-Related structure data
Related structure data | 1mq4S 2j4zS 3fdnS 3lauS 4uynS 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: 31537.053 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 Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta 2(DE3) References: UniProt: O14965, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-5VC / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.72 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 30% PEG3350, 100 mM Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127085 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 28, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.127085 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→35.95 Å / Num. all: 14214 / Num. obs: 14158 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rsym value: 0.09 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 2.18→2.22 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 1.9 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 1MQ4, 2J4Z, 3FDN, 3LAU, & 4UYN Resolution: 2.181→33.254 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.47 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.181→33.254 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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