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- PDB-5l8l: Aurora-A kinase domain in complex with vNAR-D01 (crystal form 1) -

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Basic information

Entry
Database: PDB / ID: 5l8l
TitleAurora-A kinase domain in complex with vNAR-D01 (crystal form 1)
Components
  • Aurora kinase A
  • New antigen receptor variable domain
KeywordsTRANSFERASE / kinase / vNAR / 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 / T cell receptor complex / 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 / peptide antigen binding / 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 / adaptive immune response / 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 ...: / Aurora kinase A / Aurora kinase / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Ig-like domain profile. / Immunoglobulin-like domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Immunoglobulin-like domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Aurora kinase A / New antigen receptor variable domain
Similarity search - Component
Biological speciesHomo sapiens (human)
Orectolobus maculatus (spotted wobbegong)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsBurgess, S.G. / Bayliss, R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC24461/A13231 United Kingdom
CitationJournal: Open Biology / Year: 2016
Title: Allosteric inhibition of Aurora-A kinase by a synthetic vNAR domain.
Authors: Burgess, S.G. / Oleksy, A. / Cavazza, T. / Richards, M.W. / Vernos, I. / Matthews, D. / Bayliss, R.
History
DepositionJun 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aurora kinase A
B: New antigen receptor variable domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,14115
Polymers45,7312
Non-polymers1,41013
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-70 kcal/mol
Surface area17600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.140, 84.990, 88.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 Aurora kinase A / Aurora 2 / Aurora/IPL1-related kinase 1 / hARK1 / Breast tumor-amplified kinase / Serine/threonine- ...Aurora 2 / Aurora/IPL1-related kinase 1 / hARK1 / Breast tumor-amplified kinase / Serine/threonine-protein kinase 15 / Serine/threonine-protein kinase 6 / Serine/threonine-protein kinase aurora-A


Mass: 32964.637 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
Plasmid: pET30TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL
References: UniProt: O14965, non-specific serine/threonine protein kinase
#2: Protein New antigen receptor variable domain


Mass: 12766.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orectolobus maculatus (spotted wobbegong)
Plasmid: pET26b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: Q8JJ25

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Non-polymers , 4 types, 361 molecules

#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.03 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2 M ammonium sulfate, 0.1 M sodium acetate pH 4.6, 12.5 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91741 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91741 Å / Relative weight: 1
ReflectionResolution: 1.67→45.62 Å / Num. obs: 60106 / % possible obs: 99.4 % / Redundancy: 6.7 % / CC1/2: 1 / Rmerge(I) obs: 0.046 / Net I/σ(I): 19
Reflection shellResolution: 1.67→1.71 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.3 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CEG, 2COQ

4ceg

2coq


Resolution: 1.67→44.435 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.88
RfactorNum. reflection% reflection
Rfree0.2233 2908 4.84 %
Rwork0.191 --
obs0.1925 60047 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.67→44.435 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2933 0 82 348 3363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073210
X-RAY DIFFRACTIONf_angle_d1.164372
X-RAY DIFFRACTIONf_dihedral_angle_d13.5581180
X-RAY DIFFRACTIONf_chiral_restr0.051480
X-RAY DIFFRACTIONf_plane_restr0.005556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.69740.33381520.31692665X-RAY DIFFRACTION99
1.6974-1.72670.29591630.30152643X-RAY DIFFRACTION100
1.7267-1.75810.291580.2652689X-RAY DIFFRACTION99
1.7581-1.79190.27081150.26072699X-RAY DIFFRACTION99
1.7919-1.82840.26541150.25062723X-RAY DIFFRACTION100
1.8284-1.86820.28621470.25222702X-RAY DIFFRACTION100
1.8682-1.91170.30621320.23162617X-RAY DIFFRACTION97
1.9117-1.95950.25721270.22372726X-RAY DIFFRACTION100
1.9595-2.01250.23191370.20432729X-RAY DIFFRACTION100
2.0125-2.07170.25771310.20122722X-RAY DIFFRACTION100
2.0717-2.13850.21391430.19712707X-RAY DIFFRACTION100
2.1385-2.2150.26521420.20062702X-RAY DIFFRACTION100
2.215-2.30360.22411330.20082734X-RAY DIFFRACTION100
2.3036-2.40850.22861310.19852745X-RAY DIFFRACTION100
2.4085-2.53550.24021160.22764X-RAY DIFFRACTION100
2.5355-2.69430.26321480.19282682X-RAY DIFFRACTION98
2.6943-2.90230.22171360.22698X-RAY DIFFRACTION98
2.9023-3.19430.22481500.19352766X-RAY DIFFRACTION100
3.1943-3.65630.21691290.17882785X-RAY DIFFRACTION100
3.6563-4.60580.17341460.1512783X-RAY DIFFRACTION99
4.6058-44.45070.2041570.17842858X-RAY DIFFRACTION97

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