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- PDB-5ew9: Crystal Structure of Aurora A Kinase Domain Bound to MK-5108 -

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Basic information

Entry
Database: PDB / ID: 5ew9
TitleCrystal Structure of Aurora A Kinase Domain Bound to MK-5108
ComponentsAurora kinase A
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Transferase / Protein Kinase / Inhibitor / Transferase-Transferase Inhibitor Complex
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 / positive regulation of oocyte maturation / histone H3S10 kinase activity / chromosome passenger complex / pronucleus ...Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / positive regulation of oocyte maturation / histone H3S10 kinase activity / chromosome passenger complex / pronucleus / meiotic spindle / mitotic centrosome separation / germinal vesicle / protein localization to centrosome / anterior/posterior axis specification / centrosome localization / neuron projection extension / positive regulation of mitochondrial fission / spindle organization / mitotic spindle pole / SUMOylation of DNA replication proteins / spindle midzone / regulation of G2/M transition of mitotic cell cycle / centriole / protein serine/threonine/tyrosine kinase activity / positive regulation of mitotic cell cycle / AURKA Activation by TPX2 / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of mitotic nuclear division / mitotic spindle organization / ciliary basal body / negative regulation of protein binding / regulation of signal transduction by p53 class mediator / regulation of cytokinesis / molecular function activator activity / liver regeneration / 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 / regulation of protein stability / spindle / mitotic spindle / kinetochore / response to wounding / microtubule cytoskeleton / G2/M transition of mitotic cell cycle / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / midbody / proteasome-mediated ubiquitin-dependent protein catabolic process / basolateral plasma membrane / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / microtubule / postsynaptic density / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein heterodimerization activity / cell division / negative regulation of gene expression / protein phosphorylation / protein serine kinase activity / centrosome / protein serine/threonine kinase activity / glutamatergic synapse / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Aurora kinase A / Aurora kinase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Aurora kinase A / Aurora kinase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-5VC / Aurora kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.181 Å
AuthorsShiau, A.K. / Motamedi, A.
CitationJournal: Front Oncol / Year: 2015
Title: A Cell Biologist's Field Guide to Aurora Kinase Inhibitors.
Authors: de Groot, C.O. / Hsia, J.E. / Anzola, J.V. / Motamedi, A. / Yoon, M. / Wong, Y.L. / Jenkins, D. / Lee, H.J. / Martinez, M.B. / Davis, R.L. / Gahman, T.C. / Desai, A. / Shiau, A.K.
History
DepositionNov 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aurora kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9992
Polymers31,5371
Non-polymers4621
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.851, 65.327, 77.267
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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: 31537.053 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
Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta 2(DE3)
References: UniProt: O14965, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-5VC / 4-(3-chloranyl-2-fluoranyl-phenoxy)-1-[[6-(1,3-thiazol-2-ylamino)pyridin-2-yl]methyl]cyclohexane-1-carboxylic acid / MK-5108


Mass: 461.937 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H21ClFN3O3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.72 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 30% PEG3350, 100 mM Bis-Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127085 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 28, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127085 Å / Relative weight: 1
ReflectionResolution: 2.18→35.95 Å / Num. all: 14214 / Num. obs: 14158 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rsym value: 0.09 / Net I/σ(I): 19.5
Reflection shellResolution: 2.18→2.22 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 1.9 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1MQ4, 2J4Z, 3FDN, 3LAU, & 4UYN

1mq4

2j4z

3fdn

3lau

4uyn


Resolution: 2.181→33.254 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2374 1418 10.02 %Random selection
Rwork0.1855 ---
obs0.1907 14155 99.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.181→33.254 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2084 0 31 74 2189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062178
X-RAY DIFFRACTIONf_angle_d1.1082965
X-RAY DIFFRACTIONf_dihedral_angle_d14.046800
X-RAY DIFFRACTIONf_chiral_restr0.064320
X-RAY DIFFRACTIONf_plane_restr0.004376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1813-2.25920.33551400.25961219X-RAY DIFFRACTION97
2.2592-2.34970.33271370.23291238X-RAY DIFFRACTION100
2.3497-2.45660.30161390.22731253X-RAY DIFFRACTION100
2.4566-2.58610.2711430.21871277X-RAY DIFFRACTION100
2.5861-2.7480.25631380.21721249X-RAY DIFFRACTION100
2.748-2.96010.26671400.2151263X-RAY DIFFRACTION100
2.9601-3.25770.25561430.19641277X-RAY DIFFRACTION100
3.2577-3.72860.21191430.18231288X-RAY DIFFRACTION100
3.7286-4.69550.20521440.14771301X-RAY DIFFRACTION100
4.6955-33.25750.21341510.16841372X-RAY DIFFRACTION100
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)
14.07060.39010.33242.7850.51785.42290.029-0.40220.5044-0.0786-0.17190.1792-0.94590.55430.08690.3936-0.093-0.02240.35460.00450.3511-8.105721.231614.0527
21.7906-1.36610.65823.6874-0.97473.03190.46090.2746-0.2877-0.7325-0.38090.35770.62540.2713-0.02710.46880.1014-0.1370.3406-0.05820.3229-8.0876-0.43921.8677
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ( resid 127 through 212 )
2X-RAY DIFFRACTION2chain 'A' and ( resid 213 through 390 )

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