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- PDB-3d15: Crystal structure of mouse Aurora A (Asn186->Gly, Lys240->Arg, Me... -

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Basic information

Entry
Database: PDB / ID: 3d15
TitleCrystal structure of mouse Aurora A (Asn186->Gly, Lys240->Arg, Met302->Leu) in complex with 1-(3-chloro-phenyl)-3-{5-[2-(thieno[3,2-d]pyrimidin-4-ylamino)- ethyl]-thiazol-2-yl}-urea [SNS-314]
Componentsserine/threonine kinase 6
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 / Regulation of PLK1 Activity at G2/M Transition / Regulation of TP53 Activity through Phosphorylation / meiotic spindle organization / 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 / Regulation of PLK1 Activity at G2/M Transition / Regulation of TP53 Activity through Phosphorylation / meiotic spindle organization / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / histone H3S10 kinase activity / positive regulation of oocyte maturation / mitotic centrosome separation / pronucleus / germinal vesicle / protein localization to centrosome / meiotic spindle / centrosome cycle / anterior/posterior axis specification / neuron projection extension / centrosome localization / positive regulation of mitochondrial fission / mitotic spindle pole / microtubule organizing center / liver regeneration / centriole / positive regulation of mitotic cell cycle / mitotic spindle organization / meiotic cell cycle / spindle microtubule / regulation of protein stability / response to wounding / microtubule cytoskeleton organization / spindle pole / mitotic spindle / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / basolateral plasma membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / non-specific serine/threonine protein kinase / protein kinase activity / postsynaptic density / ciliary basal body / protein heterodimerization activity / negative regulation of gene expression / cell division / protein serine kinase activity / apoptotic process / ubiquitin protein ligase binding / centrosome / protein kinase binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / glutamatergic synapse / nucleoplasm / ATP binding / cytosol
Similarity search - Function
Aurora kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-AK2 / Aurora kinase A / Aurora kinase A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsElling, R.A. / Bui, M. / Allen, D.A. / Oslob, J.D. / Romanowski, M.J.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2008
Title: Discovery of a potent and selective aurora kinase inhibitor.
Authors: Oslob, J.D. / Romanowski, M.J. / Allen, D.A. / Baskaran, S. / Bui, M. / Elling, R.A. / Flanagan, W.M. / Fung, A.D. / Hanan, E.J. / Harris, S. / Heumann, S.A. / Hoch, U. / Jacobs, J.W. / Lam, ...Authors: Oslob, J.D. / Romanowski, M.J. / Allen, D.A. / Baskaran, S. / Bui, M. / Elling, R.A. / Flanagan, W.M. / Fung, A.D. / Hanan, E.J. / Harris, S. / Heumann, S.A. / Hoch, U. / Jacobs, J.W. / Lam, J. / Lawrence, C.E. / McDowell, R.S. / Nannini, M.A. / Shen, W. / Silverman, J.A. / Sopko, M.M. / Tangonan, B.T. / Teague, J. / Yoburn, J.C. / Yu, C.H. / Zhong, M. / Zimmerman, K.M. / O'Brien, T. / Lew, W.
History
DepositionMay 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Oct 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 1.4Aug 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)31,9802
Polymers31,5491
Non-polymers4311
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.353, 82.353, 171.999
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


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) / 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-AK2 / 1-(3-chlorophenyl)-3-{5-[2-(thieno[3,2-d]pyrimidin-4-ylamino)ethyl]-1,3-thiazol-2-yl}urea


Mass: 430.934 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H15ClN6OS2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.62 Å3/Da / Density % sol: 53.12 %
Crystal growTemperature: 293 K
Details: Protein at 8.5 mg/ml in 50 mM Tris pH 7.0, 200 mM NaCl, 3 mM DTT, hanging-drop, vapor diffusion, mother liquor:bis-Tris propane ph 7.0, 35% tacsimate, temperature:293K, cryoprotectant: ...Details: Protein at 8.5 mg/ml in 50 mM Tris pH 7.0, 200 mM NaCl, 3 mM DTT, hanging-drop, vapor diffusion, mother liquor:bis-Tris propane ph 7.0, 35% tacsimate, temperature:293K, cryoprotectant:tacsimate, crystal frozen by immersion in liquid nitrogen

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 28, 2008
Details: Vertical focusing mirror; single crystal (Si111) bent monochromator (horizontal focusing)
RadiationMonochromator: side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 16029 / Num. obs: 15885 / % possible obs: 99.1 % / Redundancy: 5 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 17.3
Reflection shellResolution: 2.3→2.4 Å / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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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 1mq4

1mq4


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.916 / SU B: 8.412 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.345 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2875 1131 7.1 %RANDOM
Rwork0.23359 ---
obs0.23752 14701 98.97 %-
all-16038 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.147 Å2
Baniso -1Baniso -2Baniso -3
1--1.77 Å2-0.89 Å20 Å2
2---1.77 Å20 Å2
3---2.66 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2095 0 28 115 2238
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222179
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.331.9752948
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4785254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.17722.736106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.87515374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0731519
X-RAY DIFFRACTIONr_chiral_restr0.0770.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021667
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.2942
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.21456
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2121
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8912.51314
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.52252053
X-RAY DIFFRACTIONr_scbond_it2.7742.51004
X-RAY DIFFRACTIONr_scangle_it4.2195895
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.38 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.388 98 -
Rwork0.306 1392 -
obs--99.73 %

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