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- PDB-2wtw: Aurora-A Inhibitor Structure (2nd crystal form) -

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Basic information

Entry
Database: PDB / ID: 2wtw
TitleAurora-A Inhibitor Structure (2nd crystal form)
ComponentsSERINE/THREONINE-PROTEIN KINASE 6 AURORA/IPL1-RELATED KINASE 1, BREAST TUMOR-AMPLIFIED KINASE, AURORA-A, AURORA-RELATED KINASE 1, HARK1
KeywordsTRANSFERASE / KINASE / CELL CYCLE / PHOSPHOPROTEIN / PROTEIN KINASE
Function / homology
Function and homology information


Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / positive regulation of oocyte maturation / histone H3S10 kinase activity / chromosome passenger complex / pronucleus ...Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / positive regulation of oocyte maturation / histone H3S10 kinase activity / chromosome passenger complex / pronucleus / meiotic spindle / mitotic centrosome separation / germinal vesicle / protein localization to centrosome / anterior/posterior axis specification / centrosome localization / neuron projection extension / positive regulation of mitochondrial fission / spindle organization / mitotic spindle pole / SUMOylation of DNA replication proteins / spindle midzone / regulation of G2/M transition of mitotic cell cycle / centriole / protein serine/threonine/tyrosine kinase activity / positive regulation of mitotic cell cycle / AURKA Activation by TPX2 / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of mitotic nuclear division / mitotic spindle organization / ciliary basal body / negative regulation of protein binding / regulation of signal transduction by p53 class mediator / regulation of cytokinesis / molecular function activator activity / liver regeneration / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / regulation of protein stability / spindle / mitotic spindle / kinetochore / response to wounding / microtubule cytoskeleton / G2/M transition of mitotic cell cycle / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / midbody / proteasome-mediated ubiquitin-dependent protein catabolic process / basolateral plasma membrane / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / microtubule / postsynaptic density / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein heterodimerization activity / cell division / negative regulation of gene expression / protein phosphorylation / protein serine kinase activity / centrosome / protein serine/threonine kinase activity / glutamatergic synapse / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Aurora kinase A / 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 ...Aurora kinase A / 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-ZZL / Aurora kinase A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.302 Å
AuthorsKosmopoulou, M. / Bayliss, R.
CitationJournal: Biochem.J. / Year: 2010
Title: Crystal Structure of an Aurora-A Mutant that Mimics Aurora-B Bound to Mln8054: Insights Into Selectivity and Drug Design.
Authors: Dodson, C.A. / Kosmopoulou, M. / Richards, M.W. / Atrash, B. / Bavetsias, V. / Blagg, J. / Bayliss, R.
History
DepositionSep 24, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 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_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SERINE/THREONINE-PROTEIN KINASE 6 AURORA/IPL1-RELATED KINASE 1, BREAST TUMOR-AMPLIFIED KINASE, AURORA-A, AURORA-RELATED KINASE 1, HARK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4702
Polymers32,9931
Non-polymers4771
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.038, 84.038, 171.056
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein SERINE/THREONINE-PROTEIN KINASE 6 AURORA/IPL1-RELATED KINASE 1, BREAST TUMOR-AMPLIFIED KINASE, AURORA-A, AURORA-RELATED KINASE 1, HARK1


Mass: 32992.816 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 122-403 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET M11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS RPIL
References: UniProt: O14965, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ZZL / 4-{[9-CHLORO-7-(2,6-DIFLUOROPHENYL)-5H-PYRIMIDO[5,4-D][2]BENZAZEPIN-2-YL]AMINO}BENZOIC ACID


Mass: 476.862 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H15ClF2N4O2
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 215 TO ARG ENGINEERED RESIDUE IN CHAIN A, THR 217 TO GLU ...ENGINEERED RESIDUE IN CHAIN A, LEU 215 TO ARG ENGINEERED RESIDUE IN CHAIN A, THR 217 TO GLU ENGINEERED RESIDUE IN CHAIN A, ARG 220 TO LYS
Sequence detailsL215R, T217E, R220K MUTATIONS TO MIMIC AURORA-B, N- TERMINAL 'GAM' SEQUENCE FROM VECTOR

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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: 2.65 Å3/Da / Density % sol: 53.56 % / Description: NONE
Crystal growDetails: 0.1M MES SODIUM SALT PH6.5, 2.0M AMMONIUM SULFATE, 5%(W/V) PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.3→72.9 Å / Num. obs: 5790 / % possible obs: 99.6 % / Observed criterion σ(I): 6 / Redundancy: 14.8 % / Biso Wilson estimate: 76.38 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 20.6
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 14.8 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 7.7 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DWB

2dwb


Resolution: 3.302→66.97 Å / SU ML: 0.39 / σ(F): 0.09 / Phase error: 24.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2883 265 4.6 %
Rwork0.2339 --
obs0.2363 5738 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.397 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso mean: 76.73 Å2
Baniso -1Baniso -2Baniso -3
1--8.2733 Å20 Å20 Å2
2---8.2733 Å2-0 Å2
3---16.5465 Å2
Refinement stepCycle: LAST / Resolution: 3.302→66.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2070 0 34 0 2104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042161
X-RAY DIFFRACTIONf_angle_d0.822928
X-RAY DIFFRACTIONf_dihedral_angle_d20.183792
X-RAY DIFFRACTIONf_chiral_restr0.054309
X-RAY DIFFRACTIONf_plane_restr0.003373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3023-4.16050.29191310.23092628X-RAY DIFFRACTION98
4.1605-66.98340.28561340.23462845X-RAY DIFFRACTION99

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