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- PDB-5drd: Aurora A Kinase in Complex with ATP in Space Group P6122 -

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Basic information

Entry
Database: PDB / ID: 5drd
TitleAurora A Kinase in Complex with ATP in Space Group P6122
ComponentsAurora kinase A
KeywordsTRANSFERASE / Aurora A kinase / mitotic kinase / PPI
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 / chromosome passenger complex / positive regulation of oocyte maturation / pronucleus / mitotic centrosome separation ...Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / chromosome passenger complex / positive regulation of oocyte maturation / pronucleus / mitotic centrosome separation / germinal vesicle / meiotic spindle / 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 / negative regulation of protein binding / centriole / protein serine/threonine/tyrosine kinase activity / positive regulation of mitotic nuclear division / positive regulation of mitotic cell cycle / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / molecular function activator activity / AURKA Activation by TPX2 / regulation of cytokinesis / liver regeneration / regulation of signal transduction by p53 class mediator / mitotic spindle organization / 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 / kinetochore / response to wounding / spindle / spindle pole / G2/M transition of mitotic cell cycle / mitotic spindle / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / peptidyl-serine phosphorylation / microtubule cytoskeleton / midbody / protein autophosphorylation / basolateral plasma membrane / Regulation of TP53 Activity through Phosphorylation / microtubule / proteasome-mediated ubiquitin-dependent protein catabolic process / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / postsynaptic density / ciliary basal body / protein phosphorylation / protein heterodimerization activity / cell division / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / centrosome / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Aurora kinase A / 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 ...Aurora kinase A / 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
ADENOSINE-5'-TRIPHOSPHATE / Aurora kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsJanecek, M. / Rossmann, M. / Sharma, P. / Emery, A. / McKenzie, G.J. / Huggins, D.J. / Stockwell, S. / Stokes, J.A. / Almeida, E.G. / Hardwick, B. ...Janecek, M. / Rossmann, M. / Sharma, P. / Emery, A. / McKenzie, G.J. / Huggins, D.J. / Stockwell, S. / Stokes, J.A. / Almeida, E.G. / Hardwick, B. / Narvaez, A.J. / Hyvonen, M. / Spring, D.R. / Venkitaraman, A.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome TrustStrategic Award 090340/Z/09/Z United Kingdom
CitationJournal: Sci Rep / Year: 2016
Title: Allosteric modulation of AURKA kinase activity by a small-molecule inhibitor of its protein-protein interaction with TPX2.
Authors: Janecek, M. / Rossmann, M. / Sharma, P. / Emery, A. / Huggins, D.J. / Stockwell, S.R. / Stokes, J.E. / Tan, Y.S. / Almeida, E.G. / Hardwick, B. / Narvaez, A.J. / Hyvonen, M. / Spring, D.R. / ...Authors: Janecek, M. / Rossmann, M. / Sharma, P. / Emery, A. / Huggins, D.J. / Stockwell, S.R. / Stokes, J.E. / Tan, Y.S. / Almeida, E.G. / Hardwick, B. / Narvaez, A.J. / Hyvonen, M. / Spring, D.R. / McKenzie, G.J. / Venkitaraman, A.R.
History
DepositionSep 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aurora kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3393
Polymers31,8081
Non-polymers5312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-13 kcal/mol
Surface area12410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.610, 81.610, 166.450
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 / hARK1 / Breast tumor-amplified kinase / Serine/threonine- ...Aurora 2 / Aurora/IPL1-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: 31807.529 Da / Num. of mol.: 1 / Fragment: UNP residues 126-390
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 BL21(DE3) (bacteria) / Variant (production host): pUBS520
References: UniProt: O14965, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.74 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 100 mM HEPES pH 7.4, 200 mM magnesium sulfate, 2-20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.13→70.68 Å / Num. obs: 19152 / % possible obs: 100 % / Redundancy: 18.4 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 17.9
Reflection shellResolution: 2.13→2.19 Å / Redundancy: 19.4 % / Rmerge(I) obs: 1.773 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
PHASERphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FDN

3fdn


Resolution: 2.13→70.68 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.935 / SU ML: 0.169 / Cross valid method: FREE R-VALUE / ESU R: 0.213 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26163 965 5.1 %RANDOM
Rwork0.20592 ---
obs0.20862 18123 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.809 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å2-0 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 2.13→70.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2120 0 32 0 2152
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192213
X-RAY DIFFRACTIONr_bond_other_d0.0020.022111
X-RAY DIFFRACTIONr_angle_refined_deg1.9811.9832997
X-RAY DIFFRACTIONr_angle_other_deg1.04434857
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8275258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.2122.762105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.59315386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8111519
X-RAY DIFFRACTIONr_chiral_restr0.0970.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212426
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02528
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.9395.6141038
X-RAY DIFFRACTIONr_mcbond_other4.9315.6091037
X-RAY DIFFRACTIONr_mcangle_it6.6558.3981294
X-RAY DIFFRACTIONr_mcangle_other6.6548.4051295
X-RAY DIFFRACTIONr_scbond_it6.0586.1831172
X-RAY DIFFRACTIONr_scbond_other6.0556.1811173
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.6789.0331703
X-RAY DIFFRACTIONr_long_range_B_refined10.52545.4142516
X-RAY DIFFRACTIONr_long_range_B_other10.52345.412517
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.13→2.185 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 69 -
Rwork0.394 1294 -
obs--100 %

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