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- PDB-5k3y: Crystal structure of AuroraB/INCENP in complex with BI 811283 -

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Basic information

Entry
Database: PDB / ID: 5k3y
TitleCrystal structure of AuroraB/INCENP in complex with BI 811283
Components
  • Aurora kinase B-A
  • Inner centromere protein A
KeywordsTRANSFERASE / Kinase / Inhibitor
Function / homology
Function and homology information


mitotic cytokinesis checkpoint signaling / negative regulation of cytokinesis / positive regulation of mitotic sister chromatid segregation / abscission / mitotic spindle midzone assembly / cleavage furrow formation / histone H3S10 kinase activity / chromosome passenger complex / protein localization to kinetochore / negative regulation of B cell apoptotic process ...mitotic cytokinesis checkpoint signaling / negative regulation of cytokinesis / positive regulation of mitotic sister chromatid segregation / abscission / mitotic spindle midzone assembly / cleavage furrow formation / histone H3S10 kinase activity / chromosome passenger complex / protein localization to kinetochore / negative regulation of B cell apoptotic process / positive regulation of cytokinesis / mitotic cytokinesis / chromosome, centromeric region / spindle assembly / pericentric heterochromatin / post-translational protein modification / chromosome segregation / spindle / kinetochore / 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-6Q4 / Inner centromere protein A / Aurora kinase B-A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsBader, G. / Zahn, S.K. / 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
DepositionMay 20, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 2.0Dec 7, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_name_com.name / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.details / _struct_site.pdbx_auth_seq_id / _struct_site_gen.label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)81,3886
Polymers80,2654
Non-polymers1,1232
Water11,025612
1
A: Aurora kinase B-A
D: Inner centromere protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6943
Polymers40,1322
Non-polymers5621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-23 kcal/mol
Surface area15350 Å2
MethodPISA
2
B: Aurora kinase B-A
C: Inner centromere protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6943
Polymers40,1322
Non-polymers5621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-22 kcal/mol
Surface area15930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.907, 67.295, 116.618
Angle α, β, γ (deg.)90.000, 96.190, 90.000
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 / AIRK2-A / XAIRK2-A / Serine/threonine-protein kinase 12-A / ...Aurora/IPL1-related kinase 2-A / AIRK2-A / XAIRK2-A / Serine/threonine-protein kinase 12-A / Serine/threonine-protein kinase aurora-B-A / xAurora-B


Mass: 33104.430 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: Enterobacteria phage L1 (virus)
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: incenp-a / Production host: Enterobacteria phage L1 (virus) / References: UniProt: O13024
#3: Chemical ChemComp-6Q4 / N-methyl-N-(1-methylpiperidin-4-yl)-4-{[4-({(1R,2S)-2-[(propan-2-yl)carbamoyl]cyclopentyl}amino)-5-(trifluoromethyl)pyrimidin-2-yl]amino}benzamide


Mass: 561.642 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H38F3N7O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 612 / 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: 2.24 Å3/Da / Density % sol: 44.98 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 22% PEG 3350, 0.1M Bis-Tris propane pH 8.0, 2 mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9801 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 21, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.497→44.151 Å / Num. obs: 109777 / % possible obs: 97.2 % / Redundancy: 2.6 % / Biso Wilson estimate: 22.43 Å2 / Rmerge(I) obs: 0.115 / Rrim(I) all: 0.138 / Rsym value: 0.115 / Net I/av σ(I): 3.524 / Net I/σ(I): 8 / Num. measured all: 288940
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.5-1.581.80.6071.1192
1.58-1.682.30.5261.2199.6
1.68-1.792.50.3881.4199.7
1.79-1.942.70.3291.1199.5
1.94-2.122.90.2311.8199.2
2.12-2.3730.1832.2198.8
2.37-2.7430.1234.2198.2
2.74-3.353.10.0936.2197.4
3.35-4.7430.0698.2194
4.74-45.6442.90.0628.9181.5

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Processing

Software
NameVersionClassification
SCALA3.2.5data scaling
BUSTER-TNT2.11.6refinement
PDB_EXTRACT3.2data extraction
MOSFLMdata processing
MOLREPphasing
RefinementResolution: 1.6→32 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.088 / SU Rfree Blow DPI: 0.084 / SU Rfree Cruickshank DPI: 0.082
RfactorNum. reflection% reflectionSelection details
Rfree0.201 4543 4.98 %RANDOM
Rwork0.18 ---
obs0.181 91285 98 %-
Displacement parametersBiso max: 111.55 Å2 / Biso mean: 30.04 Å2 / Biso min: 9.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.5397 Å20 Å2-0.1011 Å2
2--0.7613 Å20 Å2
3----0.2216 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: final / Resolution: 1.6→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5118 0 102 612 5832
Biso mean--28.82 40.28 -
Num. residues----615
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1976SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes124HARMONIC2
X-RAY DIFFRACTIONt_gen_planes777HARMONIC5
X-RAY DIFFRACTIONt_it5424HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion645SEMIHARMONIC5
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_contact6674SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5424HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg7331HARMONIC20.88
X-RAY DIFFRACTIONt_omega_torsion2.73
X-RAY DIFFRACTIONt_other_torsion16.31
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 340 4.96 %
Rwork0.226 6515 -
all-6855 -
obs--99.44 %
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)
10.67710.0862-0.06170.6492-0.25850.91750.0140.1310.0266-0.0538-0.0734-0.0076-0.0297-0.02060.0594-0.08230.0114-0.00610.00240.0065-0.05663.3369-0.101315.4093
20.2736-0.12680.39320.3995-0.32561.3071-0.0671-0.00220.0310.1133-0.0002-0.0467-0.04690.08830.0673-0.03260.0033-0.0067-0.03380.0152-0.037227.334254.632455.8021
31.8595-0.65261.00331.01191.00093.52440.0616-0.0015-0.0830.1492-0.0251-0.01510.11310.031-0.03650.01330.0940.0103-0.08770.014-0.079535.188943.362769.5299
40.12-1.35231.56921.8387-2.15331.71110.00690.0050.0456-0.0478-0.0908-0.0859-0.27310.15090.084-0.09940.0063-0.03510.03830.10590.011915.785714.90178.0885
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A88 - 248
2X-RAY DIFFRACTION2{ B|* }B79 - 248
3X-RAY DIFFRACTION3{ C|* }C803 - 837
4X-RAY DIFFRACTION4{ D|* }D805 - 840

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