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- PDB-2vgp: Crystal structure of Aurora B kinase in complex with a aminothiaz... -

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Basic information

Entry
Database: PDB / ID: 2vgp
TitleCrystal structure of Aurora B kinase in complex with a aminothiazole inhibitor
Components
  • INNER CENTROMERE PROTEIN A
  • SERINE/THREONINE-PROTEIN KINASE 12-A
KeywordsTRANSFERASE / NUCLEOTIDE-BINDING / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / COILED COIL / CELL DIVISION / KINASE / CANCER / INCENP / NUCLEUS / MITOSIS / AURORA B / METAL-BINDING / AMINOTHIAZOLE / PHOSPHORYLATION / MAGNESIUM / CELL CYCLE / CENTROMERE / MICROTUBULE
Function / homology
Function and homology information


mitotic cytokinesis checkpoint signaling / meiotic spindle midzone / negative regulation of cytokinesis / positive regulation of mitotic sister chromatid segregation / meiotic spindle midzone assembly / metaphase chromosome alignment / mitotic spindle midzone assembly / cleavage furrow formation / midbody abscission / chromosome passenger complex ...mitotic cytokinesis checkpoint signaling / meiotic spindle midzone / negative regulation of cytokinesis / positive regulation of mitotic sister chromatid segregation / meiotic spindle midzone assembly / metaphase chromosome alignment / mitotic spindle midzone assembly / cleavage furrow formation / midbody abscission / chromosome passenger complex / protein localization to kinetochore / negative regulation of B cell apoptotic process / positive regulation of cytokinesis / mitotic cytokinesis / chromosome, centromeric region / spindle midzone / pericentric heterochromatin / spindle assembly / post-translational protein modification / regulation of cytokinesis / mitotic spindle organization / spindle microtubule / chromosome segregation / kinetochore / spindle / spindle pole / cellular response to UV / chromosome / midbody / microtubule / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / protein kinase binding / chromatin / negative regulation of transcription by RNA polymerase II / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2230 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2990 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2230 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2990 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-AD6 / Inner centromere protein A / Aurora kinase B-A
Similarity search - Component
Biological speciesXENOPUS LAEVIS (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAndersen, C.B. / Wan, Y. / Chang, J.W. / Lee, C. / Liu, Y. / Sessa, F. / Villa, F. / Nallan, L. / Musacchio, A. / Gray, N.S.
CitationJournal: Acs Chem.Biol. / Year: 2008
Title: Discovery of Selective Aminothiazole Aurora Kinase Inhibitors
Authors: Andersen, C.B. / Wan, Y. / Chang, J.W. / Riggs, B. / Lee, C. / Liu, Y. / Sessa, F. / Villa, F. / Kwiatkowski, N. / Suzuki, M. / Nallan, L. / Heald, R. / Musacchio, A. / Gray, N.S.
History
DepositionNov 15, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SERINE/THREONINE-PROTEIN KINASE 12-A
B: SERINE/THREONINE-PROTEIN KINASE 12-A
C: INNER CENTROMERE PROTEIN A
D: INNER CENTROMERE PROTEIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6536
Polymers77,0294
Non-polymers6242
Water13,133729
1
A: SERINE/THREONINE-PROTEIN KINASE 12-A
D: INNER CENTROMERE PROTEIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8273
Polymers38,5152
Non-polymers3121
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-31.7 kcal/mol
Surface area18760 Å2
MethodPQS
2
B: SERINE/THREONINE-PROTEIN KINASE 12-A
C: INNER CENTROMERE PROTEIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8273
Polymers38,5152
Non-polymers3121
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-28.5 kcal/mol
Surface area19770 Å2
MethodPQS
Unit cell
Length a, b, c (Å)45.958, 67.196, 117.263
Angle α, β, γ (deg.)90.00, 96.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SERINE/THREONINE-PROTEIN KINASE 12-A / AURORA B KINASE / AURORA-B-A / AURORA/IPL1-RELATED KINASE 2-A / AIRK2-A


Mass: 33537.871 Da / Num. of mol.: 2 / Fragment: RESIDUES 78-361
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) XENOPUS LAEVIS (African clawed frog) / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q6DE08, non-specific serine/threonine protein kinase
#2: Protein/peptide INNER CENTROMERE PROTEIN A / MITOTIC PHOSPHOPROTEIN 130 / XL-INCENP


Mass: 4976.640 Da / Num. of mol.: 2 / Fragment: RESIDUES 798-840
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) XENOPUS LAEVIS (African clawed frog) / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O13024
#3: Chemical ChemComp-AD6 / 4-[(5-bromo-1,3-thiazol-2-yl)amino]-N-methylbenzamide


Mass: 312.186 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H10BrN3OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 729 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.14 Å3/Da / Density % sol: 47.15 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.8726
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.7→25 Å / Num. obs: 73913 / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.1
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.4 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BFX

2bfx


Resolution: 1.7→25 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.921 / SU B: 2.299 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.243 3920 5 %RANDOM
Rwork0.206 ---
obs0.208 73913 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å2-0.66 Å2
2--0.99 Å20 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 1.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5205 0 34 729 5968
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225432
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2161.9817332
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2265632
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.87522.594266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37815988
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4571552
X-RAY DIFFRACTIONr_chiral_restr0.0780.2752
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024163
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.22630
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.23614
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2545
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.2147
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.280
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6081.53276
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.99125137
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.57932446
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5514.52195
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.261 291
Rwork0.237 5375

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