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Yorodumi- PDB-3ha6: Crystal structure of aurora A in complex with TPX2 and compound 10 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ha6 | ||||||
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Title | Crystal structure of aurora A in complex with TPX2 and compound 10 | ||||||
Components |
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Keywords | TRANSFERASE / AURORA A / SERINE/THREONINE-PROTEIN KINASE / COFACTOR / TPX2 / INHIBITOR / PHOSPHORYLATION / ATP-BINDING / CELL CYCLE / NUCLEOTIDE-BINDING / PHOSPHOPROTEIN / NUCLEUS / Kinase | ||||||
Function / homology | Function and homology information microtubule nucleation / Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / negative regulation of microtubule depolymerization / importin-alpha family protein binding / spindle assembly involved in female meiosis I / cilium disassembly / positive regulation of oocyte maturation / spindle pole centrosome ...microtubule nucleation / Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / negative regulation of microtubule depolymerization / importin-alpha family protein binding / 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 / intercellular bridge / activation of protein kinase activity / mitotic spindle pole / SUMOylation of DNA replication proteins / mitotic spindle assembly / spindle midzone / regulation of mitotic spindle organization / 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 / negative regulation of protein binding / regulation of signal transduction by p53 class mediator / 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 pole / 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 / microtubule / Regulation of TP53 Activity through Phosphorylation / protein autophosphorylation / postsynaptic density / molecular adaptor activity / 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: 2.36 Å | ||||||
Authors | Zhao, B. / Clark, M.A. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2009 Title: Design, synthesis and selection of DNA-encoded small-molecule libraries. Authors: Clark, M.A. / Acharya, R.A. / Arico-Muendel, C.C. / Belyanskaya, S.L. / Benjamin, D.R. / Carlson, N.R. / Centrella, P.A. / Chiu, C.H. / Creaser, S.P. / Cuozzo, J.W. / Davie, C.P. / Ding, Y. ...Authors: Clark, M.A. / Acharya, R.A. / Arico-Muendel, C.C. / Belyanskaya, S.L. / Benjamin, D.R. / Carlson, N.R. / Centrella, P.A. / Chiu, C.H. / Creaser, S.P. / Cuozzo, J.W. / Davie, C.P. / Ding, Y. / Franklin, G.J. / Franzen, K.D. / Gefter, M.L. / Hale, S.P. / Hansen, N.J. / Israel, D.I. / Jiang, J. / Kavarana, M.J. / Kelley, M.S. / Kollmann, C.S. / Li, F. / Lind, K. / Mataruse, S. / Medeiros, P.F. / Messer, J.A. / Myers, P. / O'Keefe, H. / Oliff, M.C. / Rise, C.E. / Satz, A.L. / Skinner, S.R. / Svendsen, J.L. / Tang, L. / van Vloten, K. / Wagner, R.W. / Yao, G. / Zhao, B. / Morgan, B.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ha6.cif.gz | 135.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ha6.ent.gz | 113.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ha6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/3ha6 ftp://data.pdbj.org/pub/pdb/validation_reports/ha/3ha6 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31253.707 Da / Num. of mol.: 1 / Fragment: UNP residues 125-391 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AIK, ARK1, AURA, AURKA, BTAK, STK15, STK6 / Plasmid: PDEST17 TEV AURORA A 125-391 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: O14965, non-specific serine/threonine protein kinase |
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#2: Protein/peptide | Mass: 4984.162 Da / Num. of mol.: 1 / Fragment: UNP residues 1-43 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: C20orf1, C20orf2, DIL2, HCA519, TPX2 / Plasmid: PDEST17 TEV AURORA A 125-391 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9ULW0 |
#3: Chemical | ChemComp-2JZ / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.27 Å3/Da / Density % sol: 71.18 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.36→50 Å / Num. obs: 22350 / % possible obs: 84 % / Observed criterion σ(I): 2 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.36→25 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.925 / SU B: 16.787 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.305 / ESU R Free: 0.238 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.454 Å2
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Refinement step | Cycle: LAST / Resolution: 2.36→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.36→2.421 Å / Total num. of bins used: 20
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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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