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- PDB-5eyk: CRYSTAL STRUCTURE OF AURORA B IN COMPLEX WITH BI 847325 -

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Basic information

Entry
Database: PDB / ID: 5eyk
TitleCRYSTAL STRUCTURE OF AURORA B IN COMPLEX WITH BI 847325
Components
  • Aurora kinase B-A
  • Inner centromere protein A
KeywordsTRANSFERASE / KINASE / Inhibitor
Function / homology
Function and homology information


meiotic spindle midzone / mitotic cytokinesis checkpoint signaling / negative regulation of cytokinesis / positive regulation of mitotic sister chromatid segregation / meiotic spindle midzone assembly / metaphase chromosome alignment / abscission / mitotic spindle midzone assembly / cleavage furrow formation / spindle pole centrosome ...meiotic spindle midzone / mitotic cytokinesis checkpoint signaling / negative regulation of cytokinesis / positive regulation of mitotic sister chromatid segregation / meiotic spindle midzone assembly / metaphase chromosome alignment / abscission / mitotic spindle midzone assembly / cleavage furrow formation / spindle pole centrosome / histone H3S10 kinase activity / chromosome passenger complex / protein localization to kinetochore / negative regulation of B cell apoptotic process / positive regulation of cytokinesis / chromosome, centromeric region / mitotic cytokinesis / spindle assembly / spindle midzone / pericentric heterochromatin / post-translational protein modification / chromosome segregation / spindle microtubule / kinetochore / spindle / cellular response to UV / chromosome / midbody / microtubule / non-specific serine/threonine protein kinase / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / chromatin / protein kinase binding / negative regulation of transcription by RNA polymerase II / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Inner centromere protein, ARK-binding domain / Chromosome passenger complex (CPC) protein INCENP N-terminal / Inner centromere protein, ARK binding region / Chromosome passenger complex (CPC) protein INCENP N terminal / Aurora kinase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site ...Inner centromere protein, ARK-binding domain / Chromosome passenger complex (CPC) protein INCENP N-terminal / Inner centromere protein, ARK binding region / Chromosome passenger complex (CPC) protein INCENP N terminal / 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-5U5 / Inner centromere protein A / Aurora kinase B-A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.93 Å
AuthorsBader, G. / Zoephel, A.
CitationJournal: Mol.Cancer Ther. / Year: 2016
Title: Pharmacological Profile of BI 847325, an Orally Bioavailable, ATP-Competitive Inhibitor of MEK and Aurora Kinases.
Authors: Sini, P. / Gurtler, U. / Zahn, S.K. / Baumann, C. / Rudolph, D. / Baumgartinger, R. / Strauss, E. / Haslinger, C. / Tontsch-Grunt, U. / Waizenegger, I.C. / Solca, F. / Bader, G. / Zoephel, A. ...Authors: Sini, P. / Gurtler, U. / Zahn, S.K. / Baumann, C. / Rudolph, D. / Baumgartinger, R. / Strauss, E. / Haslinger, C. / Tontsch-Grunt, U. / Waizenegger, I.C. / Solca, F. / Bader, G. / Zoephel, A. / Treu, M. / Reiser, U. / Garin-Chesa, P. / Boehmelt, G. / Kraut, N. / Quant, J. / Adolf, G.R.
History
DepositionNov 25, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aurora kinase B-A
B: Aurora kinase B-A
C: Inner centromere protein A
D: Inner centromere protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5096
Polymers79,5804
Non-polymers9292
Water6,864381
1
A: Aurora kinase B-A
D: Inner centromere protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2553
Polymers39,7902
Non-polymers4651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-13 kcal/mol
Surface area14440 Å2
MethodPISA
2
B: Aurora kinase B-A
C: Inner centromere protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2553
Polymers39,7902
Non-polymers4651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-20 kcal/mol
Surface area15560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.140, 67.450, 116.760
Angle α, β, γ (deg.)90.00, 96.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aurora kinase B-A / Aurora/IPL1-related kinase 2-A / XAIRK2-A / Serine/threonine-protein kinase 12-A / Serine/threonine- ...Aurora/IPL1-related kinase 2-A / XAIRK2-A / Serine/threonine-protein kinase 12-A / Serine/threonine-protein kinase aurora-B-A / xAurora-B


Mass: 32762.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: aurkb-a, airk2-a / Production host: Escherichia coli (E. coli)
References: UniProt: Q6DE08, non-specific serine/threonine protein kinase
#2: Protein Inner centromere protein A / xIncenp / Mitotic phosphoprotein 130


Mass: 7028.057 Da / Num. of mol.: 2 / Fragment: UNP residues 790-847
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: incenp-a / Production host: Escherichia coli (E. coli) / References: UniProt: O13024
#3: Chemical ChemComp-5U5 / 3-[(3~{Z})-3-[[[4-[(dimethylamino)methyl]phenyl]amino]-phenyl-methylidene]-2-oxidanylidene-1~{H}-indol-6-yl]-~{N}-ethyl-prop-2-ynamide


Mass: 464.558 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H28N4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2 / Details: PEG 3350, Bis-Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→115.98 Å / Num. obs: 52056 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 13.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.93-2.031.70.4012190.6
2.03-2.152.40.328195.6
2.15-2.33.30.271198.1
2.3-2.493.50.161198.9
2.49-2.733.40.115198.1

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Processing

Software
NameVersionClassification
BUSTER2.9.2refinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementResolution: 1.93→19.46 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.916 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2590 5 %RANDOM
Rwork0.199 ---
obs0.2 51780 96.5 %-
Displacement parametersBiso mean: 38.72 Å2
Baniso -1Baniso -2Baniso -3
1-1.2864 Å20 Å22.0899 Å2
2---10.3714 Å20 Å2
3---9.085 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 1.93→19.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4506 0 547 381 5434
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0095295HARMONIC2
X-RAY DIFFRACTIONt_angle_deg17142HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1876SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes124HARMONIC2
X-RAY DIFFRACTIONt_gen_planes757HARMONIC5
X-RAY DIFFRACTIONt_it5295HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3
X-RAY DIFFRACTIONt_other_torsion18.62
X-RAY DIFFRACTIONt_improper_torsion4HARMONIC0
X-RAY DIFFRACTIONt_chiral_improper_torsion625SEMIHARMONIC5
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_contact6244SEMIHARMONIC4
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2878 169 4.82 %
Rwork0.2397 3340 -
all0.2419 3509 -

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