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- PDB-2vgo: Crystal structure of Aurora B kinase in complex with Reversine in... -

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Basic information

Entry
Database: PDB / ID: 2vgo
TitleCrystal structure of Aurora B kinase in complex with Reversine 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 / 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 / kinetochore / spindle / cellular response to UV / chromosome / midbody / microtubule / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / chromatin / protein kinase binding / negative regulation of transcription by RNA polymerase II / ATP binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2230 / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2230 / 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 / 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 / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-AD5 / 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
AuthorsD'Alise, A.M. / Amabile, G. / Iovino, M. / Di Giorgio, F.P. / Bartiromo, M. / Sessa, F. / Villa, F. / Musacchio, A. / Cortese, R.
CitationJournal: Mol.Cancer Ther. / Year: 2008
Title: Reversine, a Novel Aurora Kinases Inhibitor, Inhibits Colony Formation of Human Acute Myeloid Leukemia Cells.
Authors: D'Alise, A.M. / Amabile, G. / Iovino, M. / Di Giorgio, F.P. / Bartiromo, M. / Sessa, F. / Villa, F. / Musacchio, A. / Cortese, R.
History
DepositionNov 15, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 2, 2022Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / pdbx_database_status / struct_conn
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 / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)78,0106
Polymers77,2234
Non-polymers7872
Water11,277626
1
A: SERINE/THREONINE-PROTEIN KINASE 12-A
D: INNER CENTROMERE PROTEIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0053
Polymers38,6122
Non-polymers3931
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-32.7 kcal/mol
Surface area18630 Å2
MethodPQS
2
B: SERINE/THREONINE-PROTEIN KINASE 12-A
C: INNER CENTROMERE PROTEIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0053
Polymers38,6122
Non-polymers3931
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-30.6 kcal/mol
Surface area19390 Å2
MethodPQS
Unit cell
Length a, b, c (Å)45.736, 67.600, 116.631
Angle α, β, γ (deg.)90.00, 96.59, 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: 5073.755 Da / Num. of mol.: 2 / Fragment: RESIDUES 797-840
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-AD5 / N~6~-cyclohexyl-N~2~-(4-morpholin-4-ylphenyl)-9H-purine-2,6-diamine / Reversine


Mass: 393.485 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O / Comment: antagonist*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 626 / 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: 2.15 Å3/Da / Density % sol: 42.29 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9537
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.7→116 Å / Num. obs: 72884 / % possible obs: 98.5 % / Observed criterion σ(I): 3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.2
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 20.2 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BFX

2bfx


Resolution: 1.7→116.25 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.132 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 3866 5 %RANDOM
Rwork0.197 ---
obs0.199 72884 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å2-0.28 Å2
2--2.01 Å20 Å2
3----1.69 Å2
Refinement stepCycle: LAST / Resolution: 1.7→116.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5237 0 58 626 5921
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225484
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0891.9877404
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9895636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4522.727264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.85415991
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2291549
X-RAY DIFFRACTIONr_chiral_restr0.0720.2758
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024177
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1910.22680
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.23711
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.2515
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.2144
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.268
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6131.53278
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.01625170
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.54832498
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5174.52234
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
Rfree0.288 279
Rwork0.242 5157

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