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- PDB-8jmx: The crystal structure of human aurka kinase domain in complex wit... -

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Basic information

Entry
Database: PDB / ID: 8jmx
TitleThe crystal structure of human aurka kinase domain in complex with AURKA-A2
ComponentsAurora kinase A
KeywordsCYTOKINE / kinase mitosis inhibitor
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 / histone H3S10 kinase activity / chromosome passenger complex / positive regulation of oocyte maturation / pronucleus ...Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / 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 / protein localization to centrosome / anterior/posterior axis specification / centrosome localization / spindle organization / neuron projection extension / positive regulation of mitochondrial fission / mitotic spindle pole / SUMOylation of DNA replication proteins / spindle midzone / regulation of G2/M transition of mitotic cell cycle / protein serine/threonine/tyrosine kinase activity / centriole / AURKA Activation by TPX2 / positive regulation of mitotic nuclear division / positive regulation of mitotic cell cycle / mitotic spindle organization / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / ciliary basal body / regulation of cytokinesis / regulation of signal transduction by p53 class mediator / negative regulation of protein binding / molecular function activator activity / liver regeneration / 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 / mitotic spindle / kinetochore / response to wounding / spindle / G2/M transition of mitotic cell cycle / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / midbody / peptidyl-serine phosphorylation / basolateral plasma membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / Regulation of TP53 Activity through Phosphorylation / protein autophosphorylation / microtubule / postsynaptic density / non-specific serine/threonine protein kinase / protein kinase activity / protein heterodimerization activity / protein phosphorylation / 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 / nucleus / cytosol
Similarity search - Function
Aurora kinase A / Aurora kinase / 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
Similarity search - Domain/homology
Chem-E47 / Aurora kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95020177482 Å
AuthorsZhu, C.J. / Zhang, Z.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chem.Commun.(Camb.) / Year: 2023
Title: Multitarget inhibitors/probes that target LRRK2 and AURORA A kinases noncovalently and covalently.
Authors: Wang, W. / Wang, X. / Tang, G. / Zhu, C. / Xiang, M. / Xiao, Q. / Zhang, Z.M. / Gao, L. / Yao, S.Q.
History
DepositionJun 5, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release

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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)30,8902
Polymers30,5661
Non-polymers3241
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Superdex G200
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.133, 83.133, 171.452
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Aurora kinase A / Aurora 2 / Aurora/IPL1-related kinase 1 / ARK-1 / Aurora-related kinase 1 / Breast tumor-amplified ...Aurora 2 / Aurora/IPL1-related kinase 1 / ARK-1 / Aurora-related kinase 1 / Breast tumor-amplified kinase / Ipl1- and aurora-related kinase 1 / Serine/threonine-protein kinase 15 / Serine/threonine-protein kinase 6 / Serine/threonine-protein kinase Ayk1 / Serine/threonine-protein kinase aurora-A


Mass: 30566.131 Da / Num. of mol.: 1
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-E47 / 5-(4-morpholin-4-yl-7H-pyrrolo[2,3-d]pyrimidin-5-yl)-2-oxidanyl-benzaldehyde


Mass: 324.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16N4O3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.86 Å3/Da / Density % sol: 57.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl (pH 8.5), 0.2 M lithium sulfate and 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.95→44.77 Å / Num. obs: 7925 / % possible obs: 100 % / Redundancy: 24 % / Biso Wilson estimate: 94.7155242654 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 24
Reflection shellResolution: 2.95→3.05 Å / Num. unique obs: 7925 / CC1/2: 0.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
autoPROCdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95020177482→44.7619867619 Å / SU ML: 0.351404133956 / Cross valid method: FREE R-VALUE / σ(F): 1.38968714321 / Phase error: 30.1800906938
RfactorNum. reflection% reflection
Rfree0.306254454324 793 10.0063091483 %
Rwork0.222438457861 7132 -
obs0.23073303539 7925 99.9873832955 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 84.2022464107 Å2
Refinement stepCycle: LAST / Resolution: 2.95020177482→44.7619867619 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1956 0 0 0 1956
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01057145003072006
X-RAY DIFFRACTIONf_angle_d1.5658504282736
X-RAY DIFFRACTIONf_chiral_restr0.0567331174225304
X-RAY DIFFRACTIONf_plane_restr0.00628765506636351
X-RAY DIFFRACTIONf_dihedral_angle_d17.0873865665708
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9503-3.1350.3385987873521270.2854045512511143X-RAY DIFFRACTION100
3.135-3.3770.3398640135541270.2609065077311143X-RAY DIFFRACTION100
3.377-3.71670.3192709370331310.2473785643041171X-RAY DIFFRACTION100
3.7167-4.25410.3331142239621300.215375696311172X-RAY DIFFRACTION99.9232540292
4.2541-5.35830.2729207991231340.2072778386821204X-RAY DIFFRACTION100
5.3583-44.750.2994739898091440.2134528194891299X-RAY DIFFRACTION100

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