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- PDB-3d2k: Crystal structure of mouse Aurora A (Asn186->Gly, Lys240->Arg, Me... -

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Basic information

Entry
Database: PDB / ID: 3d2k
TitleCrystal structure of mouse Aurora A (Asn186->Gly, Lys240->Arg, Met302->Leu) in complex with [7-(2-{2-[3-(3-chloro-phenyl)-ureido]-thiazol-5-yl}-ethylamino)-pyrazolo[4,3-d]pyrimidin-1-yl]-acetic acid
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 / meiotic spindle organization / AURKA Activation by TPX2 / 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 / meiotic spindle organization / AURKA Activation by TPX2 / 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 / histone H3S10 kinase activity / chromosome passenger complex / positive regulation of oocyte maturation / pronucleus / mitotic centrosome separation / meiotic spindle / germinal vesicle / centrosome cycle / protein localization to centrosome / microtubule organizing center / anterior/posterior axis specification / centrosome localization / neuron projection extension / positive regulation of mitochondrial fission / mitotic spindle pole / spindle midzone / centriole / positive regulation of mitotic cell cycle / mitotic spindle organization / ciliary basal body / regulation of cytokinesis / meiotic cell cycle / spindle microtubule / liver regeneration / regulation of protein stability / mitotic spindle / kinetochore / response to wounding / microtubule cytoskeleton organization / spindle pole / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / basolateral plasma membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / postsynaptic density / non-specific serine/threonine protein kinase / protein kinase activity / protein heterodimerization activity / cell division / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / negative regulation of apoptotic process / apoptotic process / protein kinase binding / perinuclear region of cytoplasm / nucleoplasm / ATP binding / 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-AK4 / Aurora kinase A / Aurora kinase A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsElling, R.A. / Oslob, 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)32,0222
Polymers31,5491
Non-polymers4731
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.310, 83.310, 77.586
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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) / Description: N-TERMINAL GST FUSION / 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-AK4 / (7-{[2-(2-{[(3-chlorophenyl)carbamoyl]amino}-1,3-thiazol-5-yl)ethyl]amino}-1H-pyrazolo[4,3-d]pyrimidin-1-yl)acetic acid


Mass: 472.908 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H17ClN8O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.13 Å3/Da / Density % sol: 42.35 %
Crystal growTemperature: 293 K / pH: 7
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: 0.1 M bis-Tris propane pH 7.0 and 1.8 M sodium acetate trihydrate; temperature: ...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: 0.1 M bis-Tris propane pH 7.0 and 1.8 M sodium acetate trihydrate; temperature: 293K; cryoprotectant: 20% glycerol; crystal frozen by immersion in liquid nitrogen.

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Data collection

DiffractionMean temperature: 160 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 29, 2006
RadiationMonochromator: Double-crystal, Si(111) liquid nitrogen-cooled
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 9951 / Num. obs: 9926 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 7.2
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 2.8 / % 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 3d14

3d14


Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.87 / SU B: 9.7 / SU ML: 0.225 / Cross valid method: THROUGHOUT / ESU R: 1.113 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27284 987 10 %RANDOM
Rwork0.21757 ---
obs0.22315 8908 99.97 %-
all-9926 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.364 Å2
Baniso -1Baniso -2Baniso -3
1--1.9 Å20 Å20 Å2
2---1.9 Å20 Å2
3---3.79 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 32 60 2093
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222085
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2621.9772826
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2255242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24623.069101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.26315348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.951516
X-RAY DIFFRACTIONr_chiral_restr0.080.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021597
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.2918
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21400
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.275
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1332.51247
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.90251965
X-RAY DIFFRACTIONr_scbond_it3.0962.5965
X-RAY DIFFRACTIONr_scangle_it4.6695861
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.586 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.291 93 -
Rwork0.183 862 -
obs--100 %

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