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Yorodumi- PDB-3dj5: Crystal structure of the mouse Aurora-A catalytic domain (Asn186-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dj5 | ||||||
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Title | Crystal structure of the mouse Aurora-A catalytic domain (Asn186->Gly, Lys240->Arg, Met302->Leu) in complex with Compound 290. | ||||||
Components | serine/threonine kinase 6 | ||||||
Keywords | TRANSFERASE / Aurora A / small-molecule inhibitor / fragment-based drug discovery / Kinase | ||||||
Function / homology | Function and homology information Interaction between PHLDA1 and AURKA / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / AURKA Activation by TPX2 / meiotic spindle organization / Regulation of PLK1 Activity at G2/M Transition / Regulation of TP53 Activity through Phosphorylation / axon hillock / spindle assembly involved in female meiosis I ...Interaction between PHLDA1 and AURKA / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / AURKA Activation by TPX2 / meiotic spindle organization / Regulation of PLK1 Activity at G2/M Transition / Regulation of TP53 Activity through Phosphorylation / 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 / centrosome cycle / protein localization to centrosome / anterior/posterior axis specification / microtubule organizing center / centrosome localization / neuron projection extension / positive regulation of mitochondrial fission / mitotic spindle pole / spindle midzone / centriole / positive regulation of mitotic cell cycle / mitotic spindle organization / ciliary basal body / regulation of cytokinesis / meiotic cell cycle / spindle microtubule / liver regeneration / regulation of protein stability / mitotic spindle / kinetochore / spindle pole / response to wounding / microtubule cytoskeleton organization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / basolateral plasma membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / postsynaptic density / non-specific serine/threonine protein kinase / protein kinase activity / protein heterodimerization activity / cell division / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / apoptotic process / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / nucleoplasm / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Elling, R.A. / Erlanson, D.A. / Yang, W. / Tangonan, B.T. / Hansen, S.K. / Romanowski, M.J. | ||||||
Citation | Journal: To be Published Title: New fragment-based drug discovery Authors: Elling, R.A. / A Erlanson, D. / Yang, W. / Tangonan, B.T. / Hansen, S.K. / Romanowski, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dj5.cif.gz | 76.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dj5.ent.gz | 55 KB | Display | PDB format |
PDBx/mmJSON format | 3dj5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/3dj5 ftp://data.pdbj.org/pub/pdb/validation_reports/dj/3dj5 | HTTPS FTP |
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-Related structure data
Related structure data | 3dj6C 3dj7C 2c6dS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 31549.174 Da / Num. of mol.: 1 / Fragment: Aurora A kinase domain, UNP residues 116-382 / Mutation: N186G, K240R, M302L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Aurka, Stk6 / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star Codon+ References: UniProt: Q8C3H8, UniProt: P97477*PLUS, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-AK5 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.77 % |
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Crystal grow | Temperature: 293 K / pH: 5.6 Details: Protein at 8.5 mg/ml in 50 mM Tris pH 7.0, 200 mM NaCl, 3 mM DTT; hanging-drop vapor diffusion; mother liquor: 0.1 M sodium citrate tribasic dihydrate pH 5.6, 2% tacsimate, 16% PEG 3350; ...Details: Protein at 8.5 mg/ml in 50 mM Tris pH 7.0, 200 mM NaCl, 3 mM DTT; hanging-drop vapor diffusion; mother liquor: 0.1 M sodium citrate tribasic dihydrate pH 5.6, 2% tacsimate, 16% PEG 3350; temperature: 293K; cryoprotectant: 20% glycerol; crystal frozen by immersion in liquid nitrogen |
-Data collection
Diffraction | Mean temperature: 160 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 29, 2008 / Details: Vertical focusing mirror |
Radiation | Monochromator: single crystal (Si111) bent monochromator (horizontal focusing) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 32098 / Num. obs: 31664 / % possible obs: 98.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.167 / Mean I/σ(I) obs: 4.9 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2c6d Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.744 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 26.476 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.863 Å / Total num. of bins used: 15
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