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- PDB-9rvk: Crystal structure of Aurora-A bound to DBL5 -

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Basic information

Entry
Database: PDB / ID: 9rvk
TitleCrystal structure of Aurora-A bound to DBL5
Components
  • Aurora kinase A
  • DBL5
KeywordsTRANSFERASE / Kinase / Complex / Designed / Inhibitor
Function / homology
Function and homology information


Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / cilium disassembly / spindle pole centrosome / mitotic centrosome separation / histone H3S10 kinase activity / chromosome passenger complex / pronucleus / regulation of G2/M transition of mitotic cell cycle ...Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / cilium disassembly / spindle pole centrosome / mitotic centrosome separation / histone H3S10 kinase activity / chromosome passenger complex / pronucleus / regulation of G2/M transition of mitotic cell cycle / germinal vesicle / meiotic spindle organization / meiotic spindle / spindle organization / positive regulation of mitochondrial fission / mitotic spindle pole / spindle midzone / SUMOylation of DNA replication proteins / negative regulation of protein binding / positive regulation of mitotic cell cycle / positive regulation of mitotic nuclear division / protein serine/threonine/tyrosine kinase activity / centriole / liver regeneration / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / AURKA Activation by TPX2 / regulation of signal transduction by p53 class mediator / molecular function activator activity / mitotic spindle organization / regulation of cytokinesis / G2/M transition of mitotic cell cycle / response to wounding / regulation of protein stability / peptidyl-serine phosphorylation / 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 / spindle / kinetochore / spindle pole / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / protein autophosphorylation / mitotic cell cycle / ciliary basal body / midbody / Regulation of TP53 Activity through Phosphorylation / basolateral plasma membrane / microtubule / protein kinase activity / protein phosphorylation / non-specific serine/threonine protein kinase / postsynaptic density / protein heterodimerization activity / negative regulation of gene expression / protein serine kinase activity / cell division / ubiquitin protein ligase binding / protein serine/threonine kinase activity / centrosome / protein kinase binding / 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
ADENOSINE-5'-DIPHOSPHATE / Aurora kinase A
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.789 Å
AuthorsMiles, J.A. / Bayliss, R.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V003577/1 United Kingdom
CitationJournal: Biorxiv / Year: 2026
Title: Selective miniprotein inhibitors of Aurora-A kinase designed using interaction-motif scaffolding
Authors: Miles, J.A. / Schiffrin, B. / Holder, J. / Wallis, E.J. / Manfield, I.W. / Burnap, S.A. / Struwe, W.B. / Gergely, F. / Bayliss, R.
History
DepositionJul 8, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DBL5
B: Aurora kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,93010
Polymers39,9202
Non-polymers1,0118
Water4,179232
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-58 kcal/mol
Surface area15120 Å2
Unit cell
Length a, b, c (Å)56.766, 68.852, 89.226
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein DBL5


Mass: 7295.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: 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: 32624.346 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

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Non-polymers , 5 types, 240 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.18 Å3/Da / Density % sol: 43.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M TRIS pH 8.5, 0.1M BICINE pH 8.5, 12.5% MPD, 12.5% PEG 1000, 12.5% PEG 3350, 0.03M Sodium fluoride, 0.03M Sodium bromide, 0.03M Sodium iodide.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 R 1M / Detector: PIXEL / Date: Jun 29, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.789→56.77 Å / Num. obs: 33504 / % possible obs: 99.3 % / Redundancy: 13.6 % / CC1/2: 1 / Net I/σ(I): 10.7
Reflection shellResolution: 1.79→1.82 Å / Num. unique obs: 1648 / CC1/2: 0.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
xia2data reduction
DIALSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.789→54.569 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 10.028 / SU ML: 0.141 / Cross valid method: FREE R-VALUE / ESU R: 0.135 / ESU R Free: 0.131 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2383 1671 4.994 %
Rwork0.1948 31787 -
all0.197 --
obs-33458 99.25 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 39.823 Å2
Baniso -1Baniso -2Baniso -3
1-0.436 Å20 Å20 Å2
2--0.236 Å2-0 Å2
3----0.672 Å2
Refinement stepCycle: LAST / Resolution: 1.789→54.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2587 0 63 232 2882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122733
X-RAY DIFFRACTIONr_angle_refined_deg1.7871.8583705
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2485330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.205521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20910469
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.07610123
X-RAY DIFFRACTIONr_chiral_restr0.1130.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022047
X-RAY DIFFRACTIONr_nbd_refined0.2220.21345
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21850
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2218
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2380.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1610.223
X-RAY DIFFRACTIONr_mcbond_it1.8482.2411308
X-RAY DIFFRACTIONr_mcangle_it2.9184.0111636
X-RAY DIFFRACTIONr_scbond_it3.2942.5971425
X-RAY DIFFRACTIONr_scangle_it5.1264.5862067
X-RAY DIFFRACTIONr_lrange_it9.96830.7724365
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.789-1.8350.3531330.37822630.37724340.8920.87998.43880.379
1.835-1.8860.3371040.35122750.35124120.8850.89198.63180.354
1.886-1.940.34930.33321890.33323190.9020.90798.40450.334
1.94-20.3151080.321310.30122590.9250.92899.11460.297
2-2.0650.282990.24220710.24321940.9370.95498.90610.23
2.065-2.1380.2611040.23119970.23221240.950.9698.91710.217
2.138-2.2180.2951000.22619560.22920680.9380.96399.41970.205
2.218-2.3090.256920.19918440.20219560.9530.97398.97750.175
2.309-2.4110.2651060.21618080.21919270.9490.96999.32540.187
2.411-2.5290.2751120.18916960.19518150.9480.97699.61430.158
2.529-2.6650.2621010.18816250.19217360.9580.97799.4240.153
2.665-2.8260.225790.17815700.18116560.9680.97999.57730.146
2.826-3.0210.298800.19314730.19915560.9410.97699.80720.156
3.021-3.2620.196530.17213930.17314490.9750.98299.7930.146
3.262-3.5720.232780.1712790.17413590.9660.98299.85280.146
3.572-3.9920.17540.14411610.14512160.9840.98999.91780.128
3.992-4.6050.186650.13910230.14110880.9790.9891000.125
4.605-5.630.199510.1558940.1589450.9720.9851000.138
5.63-7.920.246350.2217080.2227430.9730.9791000.198
7.92-54.5690.216240.2054320.2064560.9820.9791000.196
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)
14.76930.03013.43910.8227-0.50526.19520.25380.0265-0.39420.305-0.0284-0.1710.3460.2917-0.22530.23250.0443-0.04390.2503-0.01360.217833.1245-10.6416-6.4317
20.8817-0.3579-0.23081.28931.13313.0248-0.0203-0.0076-0.11820.0278-0.02050.00140.1114-0.00460.04080.0187-0.00940.00210.1180.00940.019713.1186-8.6426-23.609
Refinement TLS groupSelection: ALL

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