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- PDB-9qvz: Adhiron-mediated Identification of a Novel and Selective Alloster... -

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Basic information

Entry
Database: PDB / ID: 9qvz
TitleAdhiron-mediated Identification of a Novel and Selective Allosteric Pocket in Aurora Kinase A
Components
  • Adhiron (JR-Adh1)
  • Aurora kinase A
KeywordsTRANSFERASE / Kinase / Inhibitor / Affimer / Adhiron
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 / 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 / histone H3S10 kinase activity / chromosome passenger complex / positive regulation of oocyte maturation / mitotic centrosome separation / pronucleus / germinal vesicle / protein localization to centrosome / meiotic spindle / anterior/posterior axis specification / spindle organization / neuron projection extension / 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 / positive regulation of mitotic nuclear division / protein serine/threonine/tyrosine kinase activity / positive regulation of mitotic cell cycle / liver regeneration / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / molecular function activator activity / AURKA Activation by TPX2 / peptidyl-serine phosphorylation / regulation of signal transduction by p53 class mediator / mitotic spindle organization / regulation of cytokinesis / centriole / regulation of protein stability / 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 / response to wounding / kinetochore / G2/M transition of mitotic cell cycle / spindle / spindle pole / mitotic spindle / protein autophosphorylation / Regulation of PLK1 Activity at G2/M Transition / mitotic cell cycle / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / microtubule cytoskeleton / midbody / Regulation of TP53 Activity through Phosphorylation / basolateral plasma membrane / protein phosphorylation / microtubule / proteasome-mediated ubiquitin-dependent protein catabolic process / protein kinase activity / non-specific serine/threonine protein kinase / postsynaptic density / ciliary basal body / protein heterodimerization activity / negative regulation of gene expression / protein serine kinase activity / cell division / 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
ADENOSINE-5'-DIPHOSPHATE / : / DI(HYDROXYETHYL)ETHER / Aurora kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsRoberts, J.R. / Tomlinson, D.C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: To Be Published
Title: Adhiron-mediated Identification of a Novel and Selective Allosteric Pocket in Aurora Kinase A
Authors: Roberts, J.R. / Holder, J. / Blinkhorne, F. / Mohan, I.A. / Cordell, P.A. / Miles, J.A. / Shami-Inkindi, G.B. / Tiede, C. / Richards, M.W. / Gaule, T.G. / Smith, C.E.L. / Gergely, F. / ...Authors: Roberts, J.R. / Holder, J. / Blinkhorne, F. / Mohan, I.A. / Cordell, P.A. / Miles, J.A. / Shami-Inkindi, G.B. / Tiede, C. / Richards, M.W. / Gaule, T.G. / Smith, C.E.L. / Gergely, F. / Bayliss, R.W. / Johnson, C.A. / Tomlinson, D.C.
History
DepositionApr 13, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 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: Aurora kinase A
B: Adhiron (JR-Adh1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,72510
Polymers44,6542
Non-polymers1,0718
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance, Binds with 2.32 KD
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-8 kcal/mol
Surface area17620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.560, 86.560, 107.990
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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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: 32884.656 Da / Num. of mol.: 1 / Mutation: C290A, C393A
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: Protein Adhiron (JR-Adh1)


Mass: 11769.356 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)
#3: 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
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
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: 2.62 Å3/Da / Density % sol: 52.97 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Molecular Dimensions (Morpheous-Fusion)Condition E6 90 mM LiNaK; 1.2 % Cholic acid derivative; 0.1 M Buffer System 2 (0.5M Sodium HEPES; 0.5M MOPS (acid)); 7.5pH; 30 % Precipitant Mix 1 (40% ...Details: Molecular Dimensions (Morpheous-Fusion)Condition E6 90 mM LiNaK; 1.2 % Cholic acid derivative; 0.1 M Buffer System 2 (0.5M Sodium HEPES; 0.5M MOPS (acid)); 7.5pH; 30 % Precipitant Mix 1 (40% v/v PEG 500 MME; 20 % w/v PEG 20000)

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.95373 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.39→36 Å / Num. obs: 18994 / % possible obs: 100 % / Redundancy: 20.2 % / Biso Wilson estimate: 91.72 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.011 / Rrim(I) all: 0.038 / Net I/av σ(I): 34.5 / Net I/σ(I): 43
Reflection shellResolution: 2.39→2.43 Å / Redundancy: 20 % / Rmerge(I) obs: 3.373 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2661 / CC1/2: 0.342 / Rpim(I) all: 1.094 / Rrim(I) all: 3.546 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
REFMACv5refinement
xia2data scaling
xia2data reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→36 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / ESU R: 0.2921 / ESU R Free: 0.3358 / Phase error: 44.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3359 984 5.18 %
Rwork0.2922 --
obs0.2944 18994 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.39→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2527 0 70 0 2597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032655
X-RAY DIFFRACTIONf_angle_d0.6223607
X-RAY DIFFRACTIONf_dihedral_angle_d21.363917
X-RAY DIFFRACTIONf_chiral_restr0.039406
X-RAY DIFFRACTIONf_plane_restr0.005459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.520.41471410.40862520X-RAY DIFFRACTION100
2.52-2.670.43031210.39392542X-RAY DIFFRACTION100
2.67-2.880.48991470.45062540X-RAY DIFFRACTION100
2.88-3.170.4451470.41092534X-RAY DIFFRACTION100
3.17-3.630.46391590.37182559X-RAY DIFFRACTION100
3.63-4.570.31091270.2782606X-RAY DIFFRACTION100
4.57-360.27171420.2442709X-RAY DIFFRACTION100

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