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Yorodumi- PDB-4prj: Aurora A kinase domain with compound 2 (N-[1-(3-cyanobenzyl)-1H-p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4prj | ||||||
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Title | Aurora A kinase domain with compound 2 (N-[1-(3-cyanobenzyl)-1H-pyrazol-4-yl]-6-(1H-pyrazol-4-yl)-1H-indazole-3-carboxamide) | ||||||
Components | Aurora kinase A | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / protein kinase / phospho-transfer / 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: 2.8 Å | ||||||
Authors | Ultsch, M. / Eigenbrot, C. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2014 Title: Property- and structure-guided discovery of a tetrahydroindazole series of interleukin-2 inducible T-cell kinase inhibitors. Authors: Burch, J.D. / Lau, K. / Barker, J.J. / Brookfield, F. / Chen, Y. / Chen, Y. / Eigenbrot, C. / Ellebrandt, C. / Ismaili, M.H. / Johnson, A. / Kordt, D. / MacKinnon, C.H. / McEwan, P.A. / ...Authors: Burch, J.D. / Lau, K. / Barker, J.J. / Brookfield, F. / Chen, Y. / Chen, Y. / Eigenbrot, C. / Ellebrandt, C. / Ismaili, M.H. / Johnson, A. / Kordt, D. / MacKinnon, C.H. / McEwan, P.A. / Ortwine, D.F. / Stein, D.B. / Wang, X. / Winkler, D. / Yuen, P.W. / Zhang, Y. / Zarrin, A.A. / Pei, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4prj.cif.gz | 120.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4prj.ent.gz | 93.8 KB | Display | PDB format |
PDBx/mmJSON format | 4prj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4prj_validation.pdf.gz | 661.8 KB | Display | wwPDB validaton report |
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Full document | 4prj_full_validation.pdf.gz | 662.7 KB | Display | |
Data in XML | 4prj_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 4prj_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/4prj ftp://data.pdbj.org/pub/pdb/validation_reports/pr/4prj | HTTPS FTP |
-Related structure data
Related structure data | 4pqnC 1mq4S 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
#1: Protein | Mass: 31138.855 Da / Num. of mol.: 1 / Fragment: kinase domain (UNP residues 124-391) / Mutation: K124A/Q154N/A203S/R251K/T287A/T288A/E336D 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) References: UniProt: O14965, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-2VU / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.55 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 30% w/v PEG1500, 0.2 M lithium sulfate, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9775 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 30, 2011 |
Radiation | Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9775 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→43.15 Å / Num. all: 8532 / Num. obs: 8498 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 86.43 Å2 / Rsym value: 0.104 / Net I/σ(I): 15 |
Reflection shell | Highest resolution: 2.8 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MQ4 Resolution: 2.8→43.15 Å / Cor.coef. Fo:Fc: 0.9243 / Cor.coef. Fo:Fc free: 0.893 / SU R Cruickshank DPI: 2.66 / Isotropic thermal model: INDIVIDUAL ATOMIC PLUS TLS / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.384 / SU Rfree Cruickshank DPI: 0.382 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 86.04 Å2
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Refine analyze | Luzzati coordinate error obs: 0.519 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→43.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→3.13 Å / Total num. of bins used: 5
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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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