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- PDB-6c2r: Aurora A ligand complex -

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Basic information

Entry
Database: PDB / ID: 6c2r
TitleAurora A ligand complex
ComponentsAurora kinase A
KeywordsTRANSFERASE / Protein kinase
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 / mitotic spindle organization / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of mitotic nuclear division / ciliary basal body / negative regulation of protein binding / regulation of cytokinesis / regulation of signal transduction by p53 class mediator / 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 / mitotic spindle / 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 / protein serine/threonine kinase activity / centrosome / 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-EG7 / Aurora kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.96 Å
AuthorsAntonysamy, S. / Pustilnik, A. / Manglicmot, D. / Froning, K. / Weichert, K. / Wasserman, S.
CitationJournal: Cancer Discov / Year: 2019
Title: Aurora A Kinase Inhibition Is Synthetic Lethal with Loss of theRB1Tumor Suppressor Gene.
Authors: Gong, X. / Du, J. / Parsons, S.H. / Merzoug, F.F. / Webster, Y. / Iversen, P.W. / Chio, L.C. / Van Horn, R.D. / Lin, X. / Blosser, W. / Han, B. / Jin, S. / Yao, S. / Bian, H. / Ficklin, C. / ...Authors: Gong, X. / Du, J. / Parsons, S.H. / Merzoug, F.F. / Webster, Y. / Iversen, P.W. / Chio, L.C. / Van Horn, R.D. / Lin, X. / Blosser, W. / Han, B. / Jin, S. / Yao, S. / Bian, H. / Ficklin, C. / Fan, L. / Kapoor, A. / Antonysamy, S. / Mc Nulty, A.M. / Froning, K. / Manglicmot, D. / Pustilnik, A. / Weichert, K. / Wasserman, S.R. / Dowless, M. / Marugan, C. / Baquero, C. / Lallena, M.J. / Eastman, S.W. / Hui, Y.H. / Dieter, M.Z. / Doman, T. / Chu, S. / Qian, H.R. / Ye, X.S. / Barda, D.A. / Plowman, G.D. / Reinhard, C. / Campbell, R.M. / Henry, J.R. / Buchanan, S.G.
History
DepositionJan 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)32,2185
Polymers31,4401
Non-polymers7784
Water1,60389
1
A: Aurora kinase A
hetero molecules

A: Aurora kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,43710
Polymers62,8802
Non-polymers1,5568
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_735y+2,x-2,-z1
Buried area4000 Å2
ΔGint-100 kcal/mol
Surface area24680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.598, 83.598, 76.159
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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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: 31440.150 Da / Num. of mol.: 1 / Fragment: residues 125-391
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: unidentified baculovirus
References: UniProt: O14965, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EG7 / (2R,4R)-1-[(3-chloro-2-fluorophenyl)methyl]-4-({3-fluoro-6-[(5-methyl-1H-pyrazol-3-yl)amino]pyridin-2-yl}methyl)-2-methylpiperidine-4-carboxylic acid


Mass: 489.945 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H26ClF2N5O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 41.87 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 100mM MES pH 4.6, 23% PEG 3350, 150mM Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.96→19.804 Å / Num. obs: 19961 / % possible obs: 99.9 % / Redundancy: 13.8 % / Biso Wilson estimate: 31.24 Å2 / Rmerge(I) obs: 0.141 / Rrim(I) all: 0.149 / Rsym value: 0.141 / Net I/av σ(I): 3.9 / Net I/σ(I): 10.9 / Num. measured all: 275445
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.96-2.0713.41.1070.73839428571.1851.1072.9100
2.07-2.1913.60.6911.13692027130.7390.6914.6100
2.19-2.3413.80.4511.63504325420.4810.4516.6100
2.34-2.5314.10.3072.43369723900.3270.3078.5100
2.53-2.7714.20.2163.43136022050.230.21611.1100
2.77-3.114.20.1365.22860620110.1440.13614.6100
3.1-3.5814.10.1165.32522017870.1220.11618.1100
3.58-4.3813.90.1015.92151115480.1060.10121.3100
4.38-6.213.60.07381649612110.0770.07322.1100
6.2-19.80411.80.04613.581986970.0490.04621.195.6

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Processing

Software
NameVersionClassification
SCALA3.2.5data scaling
BUSTER2.11.7refinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
RefinementResolution: 1.96→19.7 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / SU R Cruickshank DPI: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.164 / SU Rfree Blow DPI: 0.149 / SU Rfree Cruickshank DPI: 0.148
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1013 5.09 %RANDOM
Rwork0.184 ---
obs0.187 19912 99.9 %-
Displacement parametersBiso max: 118.46 Å2 / Biso mean: 41.64 Å2 / Biso min: 15.55 Å2
Baniso -1Baniso -2Baniso -3
1-2.7002 Å20 Å20 Å2
2--2.7002 Å20 Å2
3----5.4005 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: final / Resolution: 1.96→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2018 0 75 92 2185
Biso mean--48.48 44.09 -
Num. residues----250
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d739SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes46HARMONIC2
X-RAY DIFFRACTIONt_gen_planes312HARMONIC5
X-RAY DIFFRACTIONt_it2177HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion264SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2499SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2177HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2982HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion3.1
X-RAY DIFFRACTIONt_other_torsion17.24
LS refinement shellResolution: 1.96→2.07 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2619 151 5.3 %
Rwork0.2026 2699 -
all0.2058 2850 -
obs--99.96 %
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)
13.65512.7795-0.74286.35560.24842.2977-0.07030.1308-0.1239-0.17350.2182-0.38240.16040.2856-0.1479-0.103-0.02440.0239-0.1208-0.014-0.0379118.101-15.939-3.6539
21.92290.5361-0.41842.721-0.35160.7061-0.05380.0106-0.0859-0.02860.12890.0486-0.01290.0618-0.0751-0.1085-0.0134-0.0158-0.1135-0.01830.0117101.45-35.12445.1478
30.4190.05682.8221.79561.48132.73340.01880.08760.15010.16770.0590.2018-0.30320.1197-0.0779-0.0080.01910.0807-0.08290.01060.1575125.189-53.3579-9.3061
40.85640.3448-0.31911.0167-0.788800.0279-0.00060.04620.0322-0.05810.02520.03520.03670.03020.002-0.0960.0213-0.1296-0.01120.1303110.151-17.65835.7902
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|128 - A|212 }A128 - 212
2X-RAY DIFFRACTION2{ A|213 - A|279 A|306 - A|389 }A213 - 279
3X-RAY DIFFRACTION2{ A|213 - A|279 A|306 - A|389 }A306 - 389
4X-RAY DIFFRACTION3{ A|292 - A|305 }A292 - 305
5X-RAY DIFFRACTION4{ A|404 }A404

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