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- PDB-3w10: Aurora kinase A complexed to pyrazole aminoquinoline I -

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Basic information

Entry
Database: PDB / ID: 3w10
TitleAurora kinase A complexed to pyrazole aminoquinoline I
ComponentsAurora kinase A
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / kinase / pyrazole aminoquinoline / 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 / spindle pole centrosome / positive regulation of oocyte maturation / 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 / spindle pole centrosome / positive regulation of oocyte maturation / 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 / positive regulation of mitochondrial fission / spindle organization / 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 / AURKA Activation by TPX2 / mitotic spindle organization / positive regulation of mitotic nuclear division / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / ciliary basal body / negative regulation of protein binding / regulation of cytokinesis / 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 / regulation of protein stability / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / mitotic spindle / kinetochore / spindle / response to wounding / microtubule cytoskeleton / G2/M transition of mitotic cell cycle / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / midbody / proteasome-mediated ubiquitin-dependent protein catabolic process / basolateral plasma membrane / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / microtubule / postsynaptic density / protein autophosphorylation / 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
Aurora kinase A / Aurora kinase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Aurora kinase A / Aurora kinase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-RO9 / Aurora kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsOliveira, T.M. / Kairies, N.A. / Engh, R.A.
CitationJournal: To be Published
Title: Flexibility and multiple conformations of the activation and glycine rich loops of Aurora A accompanying inhibitor binding
Authors: Oliveira, T.M. / Kairies, N.A. / Engh, R.A.
History
DepositionNov 6, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aurora kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4852
Polymers32,1551
Non-polymers3301
Water91951
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.950, 89.950, 164.302
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Aurora kinase A / / Aurora 2 / Aurora/IPL1-related kinase 1 / ARK-1 / Aurora-related kinase 1 / hARK1 / Breast tumor- ...Aurora 2 / Aurora/IPL1-related kinase 1 / ARK-1 / Aurora-related kinase 1 / hARK1 / Breast tumor-amplified kinase / Serine/threonine-protein kinase 15 / Serine/threonine-protein kinase 6 / Serine/threonine-protein kinase aurora-A


Mass: 32154.855 Da / Num. of mol.: 1 / Fragment: Domain, UNP RESIDUES 126-403 / Mutation: T287A, T288A
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
#2: Chemical ChemComp-RO9 / 1-(3-methoxyphenyl)-N-(5-methyl-1H-pyrazol-3-yl)isoquinolin-3-amine


Mass: 330.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H18N4O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.488 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 1, 2010
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.7→26.54 Å / Num. all: 11390 / Num. obs: 10633 / % possible obs: 70 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2
Reflection shellResolution: 2.7→3 Å / % possible all: 70

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Processing

Software
NameClassification
CrystalCleardata collection
MOLREPphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→26.54 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.844 / SU B: 15.943 / SU ML: 0.325 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.777 / ESU R Free: 0.391 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30897 532 4.8 %RANDOM
Rwork0.24606 ---
obs0.24906 10000 98.02 %-
all-11390 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.357 Å2
Baniso -1Baniso -2Baniso -3
1--1.61 Å2-0.81 Å20 Å2
2---1.61 Å20 Å2
3---2.42 Å2
Refinement stepCycle: LAST / Resolution: 2.7→26.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2155 0 25 51 2231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONf_bond_refined_d0.0160.0222237
X-RAY DIFFRACTIONf_angle_refined_deg1.7121.9793025
X-RAY DIFFRACTIONf_dihedral_angle_1_deg6.8515262
X-RAY DIFFRACTIONf_dihedral_angle_2_deg34.92722.593108
X-RAY DIFFRACTIONf_dihedral_angle_3_deg21.3215392
X-RAY DIFFRACTIONf_dihedral_angle_4_deg19.5541521
X-RAY DIFFRACTIONf_chiral_restr0.1180.2320
X-RAY DIFFRACTIONf_gen_planes_refined0.0070.0211708
X-RAY DIFFRACTIONf_mcbond_it0.6961.51312
X-RAY DIFFRACTIONf_mcangle_it1.36622115
X-RAY DIFFRACTIONf_scbond_it1.9193925
X-RAY DIFFRACTIONf_scangle_it3.2894.5910
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 32 -
Rwork0.334 779 -
obs--100 %

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