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- PDB-2vrx: Structure of Aurora B kinase in complex with ZM447439 -

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Basic information

Entry
Database: PDB / ID: 2vrx
TitleStructure of Aurora B kinase in complex with ZM447439
Components
  • INNER CENTROMERE PROTEIN A
  • SERINE/THREONINE-PROTEIN KINASE 12-A
KeywordsCELL CYCLE/TRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / KINASE / NUCLEUS / MITOSIS / MAGNESIUM / CENTROMERE / MICROTUBULE / ATP-BINDING / TRANSFERASE / ANTI-CANCER DRUG TARGET / PHOSPHOPROTEIN / PROTEIN KINASE / NUCLEOTIDE-BINDING / COILED COIL / CELL DIVISION / METAL-BINDING / CELL CYCLE-TRANSFERASE complex
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 - #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 / Helix non-globular / Special / Phosphorylase Kinase; domain 1 ...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 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-447 / Inner centromere protein A / Aurora kinase B-A
Similarity search - Component
Biological speciesXENOPUS LAEVIS (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsGirdler, F. / Sessa, F. / Patercoli, S. / Villa, F. / Ridgway, E. / Musacchio, A. / Taylor, S.S.
CitationJournal: Chem.Biol. / Year: 2008
Title: Molecular Basis of Drug Resistance in Aurora Kinases.
Authors: Girdler, F. / Sessa, F. / Patercoli, S. / Villa, F. / Musacchio, A. / Taylor, S.S.
History
DepositionApr 16, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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

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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)78,2846
Polymers77,2574
Non-polymers1,0272
Water10,701594
1
A: SERINE/THREONINE-PROTEIN KINASE 12-A
D: INNER CENTROMERE PROTEIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1423
Polymers38,6292
Non-polymers5141
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-34.1 kcal/mol
Surface area18350 Å2
MethodPQS
2
B: SERINE/THREONINE-PROTEIN KINASE 12-A
C: INNER CENTROMERE PROTEIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1423
Polymers38,6292
Non-polymers5141
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-29.6 kcal/mol
Surface area19100 Å2
MethodPQS
Unit cell
Length a, b, c (Å)45.735, 67.004, 116.583
Angle α, β, γ (deg.)90.00, 96.93, 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-A / AURORA/IPL1-RELATED KINASE 2-A / AIRK2-A / PROTEIN KINASE


Mass: 33651.969 Da / Num. of mol.: 2 / Fragment: CATALYTIC KINASE DOMAIN, RESIDUES 77-361 / Source method: isolated from a natural source / Source: (natural) XENOPUS LAEVIS (African clawed frog)
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 natural source / Source: (natural) XENOPUS LAEVIS (African clawed frog) / References: UniProt: O13024
#3: Chemical ChemComp-447 / N-(4-{[6-methoxy-7-(3-morpholin-4-ylpropoxy)quinazolin-4-yl]amino}phenyl)benzamide


Mass: 513.588 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H31N5O4 / Comment: inhibitor*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 594 / 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: 42.15 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 17, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 59143 / % possible obs: 92.7 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.19
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 2 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.68 / % possible all: 92.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→115.47 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.294 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2776 5.1 %RANDOM
Rwork0.188 ---
obs0.191 52024 92.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å2-0.43 Å2
2--1.79 Å20 Å2
3----1.44 Å2
Refinement stepCycle: LAST / Resolution: 1.86→115.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5204 0 76 594 5874
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225469
X-RAY DIFFRACTIONr_bond_other_d0.0080.0225469
X-RAY DIFFRACTIONr_angle_refined_deg1.161.997384
X-RAY DIFFRACTIONr_angle_other_deg1.161.997384
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2385632
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89722.717265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.77515982
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6841550
X-RAY DIFFRACTIONr_chiral_restr0.0750.2753
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024187
X-RAY DIFFRACTIONr_gen_planes_other0.0040.024187
X-RAY DIFFRACTIONr_nbd_refined0.1960.22714
X-RAY DIFFRACTIONr_nbd_other0.1960.22714
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23686
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2547
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.2140
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.257
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6391.53261
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.07225138
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.54832528
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5414.52246
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: 1.85→1.9 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.291 181
Rwork0.248 3554

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