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- PDB-9kds: The crystal structure of human AURKA kinase domain in complex with RA1 -

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Basic information

Entry
Database: PDB / ID: 9kds
TitleThe crystal structure of human AURKA kinase domain in complex with RA1
ComponentsAurora kinase A
KeywordsCYTOKINE / 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 / chromosome passenger complex / histone H3S10 kinase activity / positive regulation of oocyte maturation / 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 / histone H3S10 kinase activity / positive regulation of oocyte maturation / mitotic centrosome separation / pronucleus / germinal vesicle / protein localization to centrosome / meiotic spindle / anterior/posterior axis specification / neuron projection extension / spindle organization / centrosome localization / positive regulation of mitochondrial fission / mitotic spindle pole / spindle midzone / SUMOylation of DNA replication proteins / negative regulation of protein binding / regulation of G2/M transition of mitotic cell cycle / liver regeneration / protein serine/threonine/tyrosine kinase activity / centriole / 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 / regulation of signal transduction by p53 class mediator / AURKA Activation by TPX2 / regulation of cytokinesis / 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 / peptidyl-serine phosphorylation / regulation of protein stability / kinetochore / response to wounding / G2/M transition of mitotic cell cycle / spindle / spindle pole / mitotic spindle / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / protein autophosphorylation / microtubule cytoskeleton / midbody / basolateral plasma membrane / Regulation of TP53 Activity through Phosphorylation / proteasome-mediated ubiquitin-dependent protein catabolic process / microtubule / protein phosphorylation / 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 / protein serine/threonine 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 / 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: 2.50011813338 Å
AuthorsZhang, Z.M. / Wang, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Cell-Active, Arginine-Targeting Irreversible Covalent Inhibitors for Non-Kinases and Kinases.
Authors: Chen, P. / Wang, L. / Wang, X. / Sun, J. / Miao, F. / Wang, Z. / Yang, F. / Xiang, M. / Gu, M. / Li, S. / Zhang, J. / Yuan, P. / Lu, X. / Zhang, Z.M. / Gao, L. / Yao, S.Q.
History
DepositionNov 4, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 22, 2025Provider: 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


Theoretical massNumber of molelcules
Total (without water)31,3871
Polymers31,3871
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.943, 81.943, 172.904
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
Components on special symmetry positions
IDModelComponents
11A-523-

HOH

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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: 31387.363 Da / Num. of mol.: 1 / Mutation: C290A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.71 Å3/Da / Density % sol: 54.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M Sodium acetate, pH 4.5, 0.2 M Li2SO4,50% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Sep 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.5→44.74 Å / Num. obs: 12486 / % possible obs: 97 % / Redundancy: 31.7 % / CC1/2: 0.988 / Net I/σ(I): 13.34
Reflection shellResolution: 2.5→2.57 Å / Num. unique obs: 12486 / CC1/2: 0.739

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.50011813338→44.7385275999 Å / SU ML: 0.331630515399 / Cross valid method: FREE R-VALUE / σ(F): 1.34748722602 / Phase error: 25.3455655403
RfactorNum. reflection% reflection
Rfree0.252831155712 1218 10.0123304562 %
Rwork0.213334245863 10947 -
obs0.217459731849 12165 96.9322709163 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.0206768325 Å2
Refinement stepCycle: LAST / Resolution: 2.50011813338→44.7385275999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2016 0 0 23 2039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003353365129962071
X-RAY DIFFRACTIONf_angle_d1.980923451852826
X-RAY DIFFRACTIONf_chiral_restr0.0697583941555312
X-RAY DIFFRACTIONf_plane_restr0.0033181989311356
X-RAY DIFFRACTIONf_dihedral_angle_d14.9245907451724
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.501-2.60020.343790510021350.261796678841208X-RAY DIFFRACTION100
2.6002-2.71850.293794586084970.261339450079881X-RAY DIFFRACTION72.0176730486
2.7185-2.86180.2728154463431370.2390608126461219X-RAY DIFFRACTION100
2.8618-3.04110.3011633649351360.2346421459921230X-RAY DIFFRACTION100
3.0411-3.27580.3304103935891360.2388427932571235X-RAY DIFFRACTION100
3.2758-3.60540.2557194815881390.2192463704261245X-RAY DIFFRACTION99.7837058399
3.6054-4.12680.2014700592651400.1848140718151254X-RAY DIFFRACTION100
4.1268-5.1980.2428944500111420.1804533151291286X-RAY DIFFRACTION100
5.198-44.730.2391573348051560.2253523317341389X-RAY DIFFRACTION99.935316947
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.068892811370.5637866925930.08097143400951.3585905851-0.9561677812522.296647815220.123493717125-0.136874235086-0.946039102256-0.2458191034280.0130291518018-0.009755048234350.7940106331140.409762146804-0.1010723455280.6097019617510.162036593180.008319147419080.446850780692-0.004991675303430.6037008603763.6264072781423.075951765213.2494600311
24.217851752211.21677688074-1.601756562941.60257410107-0.141254605413.94010747888-0.0848286683523-0.4494596768250.009492798233850.145666693160.1455444365690.08260479699370.2141858322610.154871286624-0.02968408269610.369265198430.02262525286360.02901079788710.357766031098-0.06957918341840.3658365476119.30509763435.74410971926.86406778443
34.052431766880.263035531428-1.064649409873.81354284412-1.092090182932.73346574649-0.0394439655709-0.3191109254330.476809670979-0.01568938006640.137039350711-0.336989027077-0.2530477855580.279609873825-0.07791860155880.31978746214-0.03395880835680.02475236704210.374218250677-0.1182323629010.48272061312828.295970287140.98552180961.50256652728
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 126 through 217 )
2X-RAY DIFFRACTION2chain 'A' and (resid 218 through 324 )
3X-RAY DIFFRACTION3chain 'A' and (resid 325 through 391 )

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