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- PDB-5orr: Crystal structure of Aurora-A kinase in complex with an allosteri... -

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Basic information

Entry
Database: PDB / ID: 5orr
TitleCrystal structure of Aurora-A kinase in complex with an allosterically binding fragment
ComponentsAurora kinase A
KeywordsTRANSFERASE / kinase / allosteric inhibitor / fragment
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 / pronucleus ...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 / pronucleus / mitotic centrosome separation / meiotic spindle / germinal vesicle / protein localization to centrosome / anterior/posterior axis specification / centrosome localization / spindle organization / neuron projection extension / positive regulation of mitochondrial fission / mitotic spindle pole / SUMOylation of DNA replication proteins / spindle midzone / regulation of G2/M transition of mitotic cell cycle / protein serine/threonine/tyrosine kinase activity / centriole / AURKA Activation by TPX2 / positive regulation of mitotic nuclear division / positive regulation of mitotic cell cycle / mitotic spindle organization / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / ciliary basal body / regulation of cytokinesis / regulation of signal transduction by p53 class mediator / negative regulation of protein binding / 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 / kinetochore / response to wounding / spindle / G2/M transition of mitotic cell cycle / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / midbody / peptidyl-serine phosphorylation / basolateral plasma membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / Regulation of TP53 Activity through Phosphorylation / protein autophosphorylation / microtubule / postsynaptic density / non-specific serine/threonine protein kinase / protein kinase activity / protein heterodimerization activity / protein phosphorylation / cell division / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / negative regulation of apoptotic process / 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-A5Q / ADENOSINE-5'-DIPHOSPHATE / Aurora kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.09 Å
AuthorsMcIntyre, P.J. / Collins, P.M. / von Delft, F. / Bayliss, R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Cancer Research UKC24461/A12772 United Kingdom
Cancer Research UKC24461/A23302 United Kingdom
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: Characterization of Three Druggable Hot-Spots in the Aurora-A/TPX2 Interaction Using Biochemical, Biophysical, and Fragment-Based Approaches.
Authors: McIntyre, P.J. / Collins, P.M. / Vrzal, L. / Birchall, K. / Arnold, L.H. / Mpamhanga, C. / Coombs, P.J. / Burgess, S.G. / Richards, M.W. / Winter, A. / Veverka, V. / Delft, F.V. / Merritt, A. / Bayliss, R.
History
DepositionAug 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aurora kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5907
Polymers30,7981
Non-polymers7926
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-43 kcal/mol
Surface area12640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.140, 82.140, 176.500
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 1 molecules A

#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: 30798.236 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, 105 molecules

#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-A5Q / 4-[4-(trifluoromethyl)phenyl]-1,2,3-thiadiazol-5-amine


Mass: 245.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H6F3N3S
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.79 Å3/Da / Density % sol: 55.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris, pH 8.5; 0.5 M NaCl; 0.2 M MgCl2; 32.5 % v/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.09→65.978 Å / Num. obs: 39499 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.027 % / Biso Wilson estimate: 52.611 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.115 / Rrim(I) all: 0.122 / Χ2: 1.017 / Net I/σ(I): 13.43
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.09-2.149.2552.7080.9829070.4032.868100
2.14-2.29.7642.1351.2428480.5432.254100
2.2-2.2710.671.5661.7327860.681.645100
2.27-2.3410.5941.0882.5726900.791.14399.9
2.34-2.4110.5480.9383.0526150.8490.986100
2.41-2.510.540.7543.9225100.8990.793100
2.5-2.5910.3910.5925.0924290.9390.62299.9
2.59-2.710.120.4886.3323320.9540.514100
2.7-2.829.060.3658.1722540.9710.387100
2.82-2.9610.7740.25612.0221250.9870.269100
2.96-3.1210.7080.20214.5320470.9910.212100
3.12-3.310.4670.14219.3119430.9950.14999.9
3.3-3.5310.0340.09924.7318000.9970.10599.9
3.53-3.829.4560.07329.6616830.9980.07799.8
3.82-4.188.130.05832.6815570.9980.062100
4.18-4.679.7670.04941.6213960.9980.05299.9
4.67-5.49.820.04642.0912580.9990.049100
5.4-6.619.6120.04539.8310440.9990.047100
6.61-9.358.9060.03943.228160.9990.04199.8
9.35-65.97810.3660.0349.964590.9990.03199.4

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
xia2data reduction
PHENIXphasing
RefinementResolution: 2.09→65.978 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.06
RfactorNum. reflection% reflection
Rfree0.2561 1106 5.11 %
Rwork0.199 --
obs0.2017 21633 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 155.44 Å2 / Biso mean: 52.7137 Å2 / Biso min: 29.54 Å2
Refinement stepCycle: final / Resolution: 2.09→65.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2135 0 47 99 2281
Biso mean--66.09 52.91 -
Num. residues----265
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)
13.29551.35530.63041.9045-0.07780.29270.0072-0.0055-0.3781-0.20860.0337-0.3490.21890.0922-0.07760.4539-0.01710.0310.3783-0.14120.4613-0.725822.2376-12.1845
23.00410.6549-0.77273.6256-0.54042.8197-0.31410.6921-0.8619-1.2062-0.0271-0.20930.285-1.55330.29440.6414-0.0335-0.01630.6639-0.2290.5342-16.667420.2857-16.9311
31.6689-0.5337-0.3320.48090.62411.82660.30110.7772-0.3386-0.7550.1107-0.00560.1479-0.0089-0.26030.6274-0.1046-0.00180.565-0.12330.4114-9.78629.2-19.706
41.7520.4829-0.49361.34860.46430.4093-0.193-0.00180.07690.08140.364-0.41980.15430.1072-0.12280.4272-0.0121-0.09460.4904-0.09270.4243-7.707732.6731-5.3207
52.8369-1.8134-0.00963.39230.4721.45490.0330.28640.0345-0.17950.08130.47970.0360.0006-0.0940.3767-0.0348-0.02770.4939-0.02010.4029-19.859934.7549-11.4799
62.64220.53080.46224.09150.34965.42720.38310.5019-0.54780.31860.24950.0640.7241-0.3863-0.71260.4438-0.0894-0.02980.4448-0.10090.4747-30.411426.4437-3.6419
72.30550.3845-0.47372.2754-0.38760.98240.16230.21040.23320.1243-0.19710.28650.0449-0.2498-0.13230.3420.0352-0.02850.3966-0.01580.4157-25.943438.4432-3.7308
82.7666-0.09570.99740.8492-1.11352.7015-0.3571-0.85490.13010.5694-0.0310.39750.1239-0.62890.29610.512-0.02860.10270.4677-0.07960.4386-28.781330.39597.877
91.9067-0.2317-0.44583.8192-0.30692.6726-0.01130.24170.4293-0.1924-0.02370.2763-0.4199-0.34130.03980.35110.0596-0.05140.383-0.01120.4893-30.339845.3826-4.3461
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 127 through 172 )A127 - 172
2X-RAY DIFFRACTION2chain 'A' and (resid 173 through 187 )A173 - 187
3X-RAY DIFFRACTION3chain 'A' and (resid 188 through 201 )A188 - 201
4X-RAY DIFFRACTION4chain 'A' and (resid 202 through 229 )A202 - 229
5X-RAY DIFFRACTION5chain 'A' and (resid 230 through 287 )A230 - 287
6X-RAY DIFFRACTION6chain 'A' and (resid 289 through 307 )A289 - 307
7X-RAY DIFFRACTION7chain 'A' and (resid 308 through 324 )A308 - 324
8X-RAY DIFFRACTION8chain 'A' and (resid 325 through 342 )A325 - 342
9X-RAY DIFFRACTION9chain 'A' and (resid 343 through 391 )A343 - 391

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