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- PDB-3d2i: Crystal structure of mouse Aurora A (Asn186->Gly, Lys240->Arg, Me... -

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Basic information

Entry
Database: PDB / ID: 3d2i
TitleCrystal structure of mouse Aurora A (Asn186->Gly, Lys240->Arg, Met302->Leu) in complex with 1-{5-[2-(1-methyl-1H-pyrazolo[4,3-d]pyrimidin-7-ylamino)-ethyl]-thiazol-2-yl}-3-(3-trifluoromethyl-phenyl)-urea
Componentsserine/threonine kinase 6Serine/threonine-specific protein kinase
KeywordsTRANSFERASE / Aurora A / small-molecule inhibitor / Kinase
Function / homology
Function and homology information


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 / spindle pole centrosome / positive regulation of oocyte maturation / histone H3S10 kinase activity / chromosome passenger complex / pronucleus / meiotic spindle / mitotic centrosome separation / centrosome cycle / germinal vesicle / protein localization to centrosome / anterior/posterior axis specification / microtubule organizing center / centrosome localization / neuron projection extension / positive regulation of mitochondrial fission / spindle organization / mitotic spindle pole / spindle midzone / centriole / positive regulation of mitotic cell cycle / mitotic spindle organization / ciliary basal body / meiotic cell cycle / regulation of cytokinesis / molecular function activator activity / liver regeneration / spindle microtubule / regulation of protein stability / mitotic spindle / microtubule cytoskeleton organization / kinetochore / spindle pole / response to wounding / microtubule cytoskeleton / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / proteasome-mediated ubiquitin-dependent protein catabolic process / basolateral plasma membrane / postsynaptic density / non-specific serine/threonine protein kinase / protein kinase activity / protein heterodimerization activity / cell division / phosphorylation / negative regulation of gene expression / protein serine kinase activity / centrosome / protein serine/threonine kinase activity / 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 / 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 ...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-AK3 / Aurora kinase A / Aurora kinase A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsOslob, J.D. / Yu, C. / Romanowski, M.J.
CitationJournal: To be Published
Title: Discovery of Aurora-A-selective inhibitors
Authors: Oslob, J.D. / Yu, C. / Allen, D.A. / Baskaran, S. / Maung, J. / Michelotti, E.F. / Elling, R.A. / Romanowski, M.J.
History
DepositionMay 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: serine/threonine kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0122
Polymers31,5491
Non-polymers4621
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.920, 82.920, 171.964
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 serine/threonine kinase 6 / Serine/threonine-specific protein kinase


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.) Mus musculus (house mouse) / Description: N-TERMINAL GST FUSION PROTEIN / Gene: Aurka, Stk6 / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star
References: UniProt: Q8C3H8, UniProt: P97477*PLUS, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-AK3 / 1-(5-{2-[(1-methyl-1H-pyrazolo[4,3-d]pyrimidin-7-yl)amino]ethyl}-1,3-thiazol-2-yl)-3-[3-(trifluoromethyl)phenyl]urea


Mass: 462.451 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H17F3N8OS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.7 Å3/Da / Density % sol: 54.52 %
Crystal growTemperature: 293 K / pH: 7
Details: Protein @ 8.5 mg/ml in 50 mM Tris pH 7.0, 200 mM NaCl, 3 mM DTT; hanging-drop vapor diffusion; mother liquor: 0.1 M bis-Tris propane pH 7.0 and 35% tacsimate; temperature: 293K; ...Details: Protein @ 8.5 mg/ml in 50 mM Tris pH 7.0, 200 mM NaCl, 3 mM DTT; hanging-drop vapor diffusion; mother liquor: 0.1 M bis-Tris propane pH 7.0 and 35% tacsimate; temperature: 293K; cryoprotectant: tacsimate; crystal frozen by immersion in liquid nitrogen.

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Data collection

DiffractionMean temperature: 160 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 22, 2005
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 9200 / Num. obs: 8941 / % possible obs: 97.6 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 7
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 2.2 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CrystalCleardata collection
CrystalCleardata reduction
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3D14

3d14


Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.889 / SU B: 19.793 / SU ML: 0.373 / Cross valid method: THROUGHOUT / ESU R Free: 0.478 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29839 590 7.3 %RANDOM
Rwork0.24065 ---
obs0.24492 7469 97.34 %-
all-8319 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.915 Å2
Baniso -1Baniso -2Baniso -3
1--1.88 Å2-0.94 Å20 Å2
2---1.88 Å20 Å2
3---2.81 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2058 0 32 35 2125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0212145
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.9742913
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1185253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84522.718103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.74215349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8041518
X-RAY DIFFRACTIONr_chiral_restr0.060.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021653
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1760.2912
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.21446
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0990.280
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.236
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.782.51291
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.09752038
X-RAY DIFFRACTIONr_scbond_it1.4212.5992
X-RAY DIFFRACTIONr_scangle_it2.3665874
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→3 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.348 48 -
Rwork0.294 723 -
obs--98.72 %

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