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- PDB-8jf4: The crystal structure of human AURKA kinase domain in complex wit... -

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Basic information

Entry
Database: PDB / ID: 8jf4
TitleThe crystal structure of human AURKA kinase domain in complex with AURKA-compound 9
ComponentsAurora kinase A
KeywordsCYTOKINE / Lysine 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 / positive regulation of oocyte maturation / histone H3S10 kinase activity / chromosome passenger complex / pronucleus ...Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / 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 / germinal vesicle / protein localization to centrosome / anterior/posterior axis specification / centrosome localization / neuron projection extension / positive regulation of mitochondrial fission / spindle organization / mitotic spindle pole / SUMOylation of DNA replication proteins / spindle midzone / regulation of G2/M transition of mitotic cell cycle / centriole / protein serine/threonine/tyrosine kinase activity / positive regulation of mitotic cell cycle / AURKA Activation by TPX2 / mitotic spindle organization / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of mitotic nuclear division / ciliary basal body / negative regulation of protein binding / regulation of cytokinesis / regulation of signal transduction by p53 class mediator / 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 / spindle / kinetochore / response to wounding / microtubule cytoskeleton / G2/M transition of mitotic cell cycle / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / midbody / proteasome-mediated ubiquitin-dependent protein catabolic process / basolateral plasma membrane / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / microtubule / postsynaptic density / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein heterodimerization activity / cell division / negative regulation of gene expression / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / 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 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89288354365 Å
AuthorsZhu, C.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Global Reactivity Profiling of the Catalytic Lysine in Human Kinome for Covalent Inhibitor Development.
Authors: Tang, G. / Wang, W. / Zhu, C. / Huang, H. / Chen, P. / Wang, X. / Xu, M. / Sun, J. / Zhang, C.J. / Xiao, Q. / Gao, L. / Zhang, Z.M. / Yao, S.Q.
History
DepositionMay 17, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aurora kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1162
Polymers30,5661
Non-polymers5501
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.263, 85.263, 168.357
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: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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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-C0N / 2-[4-[4-[bis(oxidanylidene)-$l^5-sulfanyl]oxyphenyl]carbonylpiperazin-1-yl]-6-[(5-cyclopropyl-1H-pyrazol-3-yl)amino]-N-prop-2-ynyl-pyrimidine-4-carboxamide


Mass: 549.582 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H25N8O5S
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: 2.89 Å3/Da / Density % sol: 57.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M lithium sulfate, 0.1 M TRIS pH 8.5, 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: 2.89→33.96 Å / Num. obs: 13750 / % possible obs: 100 % / Redundancy: 18 % / Biso Wilson estimate: 101.686906195 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.135 / Net I/σ(I): 19.3
Reflection shellResolution: 2.89→2.99 Å / Num. unique obs: 13750 / CC1/2: 0.842

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
autoPROCdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.89288354365→33.9471071719 Å / SU ML: 0.53406509141 / Cross valid method: FREE R-VALUE / σ(F): 1.35500644524 / Phase error: 36.331029926
RfactorNum. reflection% reflection
Rfree0.299660770841 1387 10.0990243192 %
Rwork0.234016952431 12347 -
obs0.24075474635 13734 89.8057935003 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70 Å2
Refinement stepCycle: LAST / Resolution: 2.89288354365→33.9471071719 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2016 0 0 0 2016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00237258858122071
X-RAY DIFFRACTIONf_angle_d0.6836577331382818
X-RAY DIFFRACTIONf_chiral_restr0.0257235439027306
X-RAY DIFFRACTIONf_plane_restr0.00215119213795359
X-RAY DIFFRACTIONf_dihedral_angle_d18.274273667737
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8929-2.99620.349646100029400.328992801248365X-RAY DIFFRACTION26.3671875
2.9962-3.11610.3717658077131150.3643499369331007X-RAY DIFFRACTION74.8998664887
3.1161-3.25780.4004037674621510.3378887489521351X-RAY DIFFRACTION97.2797927461
3.2578-3.42940.3115135390721580.304963179691391X-RAY DIFFRACTION100
3.4294-3.64410.3427277515321470.2877614954661360X-RAY DIFFRACTION100
3.6441-3.9250.325165757811610.2489538905191368X-RAY DIFFRACTION100
3.925-4.31930.3237761843911540.2174398717481374X-RAY DIFFRACTION100
4.3193-4.94270.2869006163251520.195960760651388X-RAY DIFFRACTION100
4.9427-6.2210.2758441917861530.2476967007551365X-RAY DIFFRACTION100
6.221-33.940.2635042110161560.1975355702221378X-RAY DIFFRACTION99.6751137102

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