[English] 日本語
![](img/lk-miru.gif)
- PDB-3dj6: Crystal structure of the mouse Aurora-A catalytic domain (Asn186-... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3dj6 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the mouse Aurora-A catalytic domain (Asn186->Gly, Lys240->Arg, Met302->Leu) in complex with Compound 823. | ||||||
![]() | serine/threonine kinase 6 | ||||||
![]() | TRANSFERASE / Aurora A / small-molecule inhibitor / fragment-based drug discovery / Kinase | ||||||
Function / homology | ![]() 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 / meiotic cell cycle / centriole / liver regeneration / positive regulation of mitotic cell cycle / mitotic spindle organization / ciliary basal body / regulation of cytokinesis / spindle microtubule / 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 / ubiquitin protein ligase binding / glutamatergic synapse / negative regulation of apoptotic process / protein kinase binding / apoptotic process / perinuclear region of cytoplasm / nucleoplasm / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Elling, R.A. / Erlanson, D.A. / Yang, W. / Tangonan, B.T. / Hansen, S.K. / Romanowski, M.J. | ||||||
![]() | ![]() Title: New fragment-based drug discovery Authors: Elling, R.A. / Erlanson, D.A. / Yang, W. / Tangonan, B.T. / Hansen, S.K. / Romanowski, M.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 77.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 55.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 3dj5C ![]() 3dj7C ![]() 2c6dS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
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.) ![]() ![]() ![]() ![]() References: UniProt: Q8C3H8, UniProt: P97477*PLUS, non-specific serine/threonine protein kinase |
---|---|
#2: Chemical | ChemComp-AK6 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.15 % |
---|---|
Crystal grow | Temperature: 293 K / pH: 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: 8% tacsimate pH 6.0, 20% PEG 3350; temperature: 293K; cryoprotectant: 20% ...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: 8% tacsimate pH 6.0, 20% PEG 3350; temperature: 293K; cryoprotectant: 20% glycerol; crystal frozen by immersion in liquid nitrogen |
-Data collection
Diffraction | Mean temperature: 160 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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: 1.7→30 Å / Num. all: 37500 / Num. obs: 36636 / % possible obs: 97.7 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 2 / % possible all: 90.3 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 2c6d Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.902 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 29.131 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.76 Å / Total num. of bins used: 15
|