+Open data
-Basic information
Entry | Database: PDB / ID: 4deb | ||||||
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Title | Aurora A in complex with RK2-17-01 | ||||||
Components | Aurora kinase A | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / PROTEIN KINASE / AURORA A / INHIBITOR / DFG-IN / 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 / MOLECULAR REPLACEMENT / Resolution: 3.05 Å | ||||||
Authors | Martin, M.P. / Zhu, J.-Y. / Schonbrunn, E. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2012 Title: Development of o-Chlorophenyl Substituted Pyrimidines as Exceptionally Potent Aurora Kinase Inhibitors. Authors: Lawrence, H.R. / Martin, M.P. / Luo, Y. / Pireddu, R. / Yang, H. / Gevariya, H. / Ozcan, S. / Zhu, J.Y. / Kendig, R. / Rodriguez, M. / Elias, R. / Cheng, J.Q. / Sebti, S.M. / Schonbrunn, E. / Lawrence, N.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4deb.cif.gz | 69.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4deb.ent.gz | 50.5 KB | Display | PDB format |
PDBx/mmJSON format | 4deb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4deb_validation.pdf.gz | 729.1 KB | Display | wwPDB validaton report |
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Full document | 4deb_full_validation.pdf.gz | 744.1 KB | Display | |
Data in XML | 4deb_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 4deb_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/4deb ftp://data.pdbj.org/pub/pdb/validation_reports/de/4deb | HTTPS FTP |
-Related structure data
Related structure data | 3up7C 4deaC 4dedC 4deeC 3fdnS C: citing same article (ref.) 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: 32359.123 Da / Num. of mol.: 1 / Mutation: T287D 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-MBP / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TUNER(DE3) References: UniProt: O14965, non-specific serine/threonine protein kinase | ||
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#2: Chemical | ChemComp-NHJ / | ||
#3: Chemical | #4: 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: 2.63 Å3/Da / Density % sol: 53.25 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10 mg/mL AURORA A protein, 1 mM RK2-17-01, 10 % (v/v) PEG 3350, 25 mM phosphate(Na/K pH 7.4), 100 mM sodium tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 20, 2010 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 3.05→20 Å / Num. obs: 6944 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 6.67 % / Rmerge(I) obs: 0.069 / Rsym value: 6.4 / Net I/σ(I): 26.8 |
Reflection shell | Resolution: 3.05→3.1 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 5 / Rsym value: 37.7 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3FDN Resolution: 3.05→19.73 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 3160670.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 30.0121 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.05→19.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.05→3.24 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 6
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Xplor file |
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