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- PDB-9ks6: The crystal structure of AURKA in complex with K-CNBA-1 -

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Basic information

Entry
Database: PDB / ID: 9ks6
TitleThe crystal structure of AURKA in complex with K-CNBA-1
ComponentsAurora kinase A
KeywordsUNKNOWN FUNCTION / AURKA / K-CNBA-1 / lysine modification / Irreversible covalent probe
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 / protein serine/threonine/tyrosine kinase activity / liver regeneration / 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 / mitotic spindle organization / regulation of cytokinesis / 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 / 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 / Regulation of TP53 Activity through Phosphorylation / basolateral plasma membrane / 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: 2.75 Å
AuthorsZhang, Z.M. / Duan, L.P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: O-Cyanobenzaldehydes (CNBA) Irreversibly Modify both Buried and Exposed Lysine Residues in Live Cells
Authors: Zhang, Z.M. / Duan, L.P.
History
DepositionNov 29, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 3, 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)31,2591
Polymers31,2591
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.93, 81.93, 169.031
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: 31258.877 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
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: 2.52 Å3/Da / Density % sol: 51.19 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M Sodium acetate (pH 5.0), 0.2 M lithium sulfate and 40% w/v PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 0.978 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: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.75→45 Å / Num. obs: 8936 / % possible obs: 95.4 % / Redundancy: 34.9 % / Biso Wilson estimate: 70.7920027222 Å2 / CC1/2: 0.997 / Net I/σ(I): 16.5
Reflection shellResolution: 2.75→2.9 Å / Num. unique obs: 1317 / CC1/2: 0.953

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
HKL-3000data reduction
HKL-3000data scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→44.12 Å / SU ML: 0.367471538633 / Cross valid method: FREE R-VALUE / σ(F): 1.33792845058 / Phase error: 28.0098752694
RfactorNum. reflection% reflection
Rfree0.266917947575 887 9.99887273137 %
Rwork0.228170897466 7984 -
obs0.232151662593 8871 95.2846401719 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.3257370184 Å2
Refinement stepCycle: LAST / Resolution: 2.75→44.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1988 0 38 0 2026
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002305127295912084
X-RAY DIFFRACTIONf_angle_d0.6238391861992833
X-RAY DIFFRACTIONf_chiral_restr0.0237984723142308
X-RAY DIFFRACTIONf_plane_restr0.00235588207913360
X-RAY DIFFRACTIONf_dihedral_angle_d13.1493108314746
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.92240.3566716747641490.2724755333851349X-RAY DIFFRACTION99.9332888592
2.9224-3.1480.3168769952471510.2730681978191354X-RAY DIFFRACTION100
3.148-3.46470.3187063394791360.262328576111218X-RAY DIFFRACTION89.1963109354
3.4647-3.96580.2840672706081250.2117497221321138X-RAY DIFFRACTION82.5490196078
3.9658-4.99530.2158212015891570.1962100166941401X-RAY DIFFRACTION99.8078155029
4.9953-44.120.2620595281841690.2350074280381524X-RAY DIFFRACTION99.7642899234
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)
18.21537265467-0.3493165820620.217335496146.864234415982.720050512416.667057848390.1013258900210.4038271263290.810536963361-0.5458778476820.2261796932590.00619775724158-1.30212905061-0.395436071748-0.136783807160.6199130836910.08997114617420.06539573700970.5697859316930.01759938330010.6929566465273.79457518833-23.374394149611.3796028573
26.24039779754-1.174184181230.7723925792547.03607133975-1.123015109025.71306275740.316780483231-0.3158308945411.31670819344-0.5488789287370.133100132410.140979106582-0.763644756343-1.11437326379-0.4479244287730.9398907265220.1457637640060.02377085453350.553608315944-0.05376248001280.875936715032-9.97119782802-18.272523038612.3061435296
36.096789940381.126634592941.660775178884.19996880453.463989651974.61453705727-0.0431978878642-0.2303235495560.2096037860280.001905755267720.105703824899-0.173682459872-0.241109079953-0.390589138078-0.06105876628130.4740063035960.121761285674-0.04614181455970.4070296381210.1029196787920.467711704656-11.5877689064-34.397767117210.3846764301
46.024279620730.2177726308320.7203970320597.66260006662-1.334996167557.72062904128-0.0305505385477-0.781747677643-0.1815294946860.1651204639230.102758880570.405009257753-0.153220767499-0.399096596261-0.08608662529770.3141010555220.0179769940104-0.004770471880180.5128302814890.1302753077130.540251664269-27.3187975954-37.7762511892.87324620724
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 127 through 156 )
2X-RAY DIFFRACTION2chain 'A' and (resid 157 through 186 )
3X-RAY DIFFRACTION3chain 'A' and (resid 187 through 272 )
4X-RAY DIFFRACTION4chain 'A' and (resid 273 through 391 )

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