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- PDB-3dj5: Crystal structure of the mouse Aurora-A catalytic domain (Asn186-... -

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Basic information

Entry
Database: PDB / ID: 3dj5
TitleCrystal structure of the mouse Aurora-A catalytic domain (Asn186->Gly, Lys240->Arg, Met302->Leu) in complex with Compound 290.
Componentsserine/threonine kinase 6
KeywordsTRANSFERASE / Aurora A / small-molecule inhibitor / fragment-based drug discovery / Kinase
Function / homology
Function and homology information


Interaction between PHLDA1 and AURKA / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / AURKA Activation by TPX2 / Regulation of PLK1 Activity at G2/M Transition / Regulation of TP53 Activity through Phosphorylation / meiotic spindle organization / axon hillock / spindle assembly involved in female meiosis I ...Interaction between PHLDA1 and AURKA / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / AURKA Activation by TPX2 / Regulation of PLK1 Activity at G2/M Transition / Regulation of TP53 Activity through Phosphorylation / meiotic spindle organization / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / histone H3S10 kinase activity / positive regulation of oocyte maturation / mitotic centrosome separation / pronucleus / germinal vesicle / protein localization to centrosome / meiotic spindle / centrosome cycle / anterior/posterior axis specification / neuron projection extension / centrosome localization / positive regulation of mitochondrial fission / mitotic spindle pole / microtubule organizing center / liver regeneration / centriole / positive regulation of mitotic cell cycle / mitotic spindle organization / meiotic cell cycle / spindle microtubule / regulation of protein stability / response to wounding / microtubule cytoskeleton organization / spindle pole / mitotic spindle / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / basolateral plasma membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / non-specific serine/threonine protein kinase / protein kinase activity / postsynaptic density / ciliary basal body / protein heterodimerization activity / negative regulation of gene expression / cell division / protein serine kinase activity / apoptotic process / ubiquitin protein ligase binding / centrosome / protein kinase binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / glutamatergic synapse / nucleoplasm / ATP binding / cytosol
Similarity search - Function
Aurora kinase / 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 ...Aurora kinase / 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-AK5 / Aurora kinase A / Aurora kinase A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsElling, R.A. / Erlanson, D.A. / Yang, W. / Tangonan, B.T. / Hansen, S.K. / Romanowski, M.J.
CitationJournal: To be Published
Title: New fragment-based drug discovery
Authors: Elling, R.A. / A Erlanson, D. / Yang, W. / Tangonan, B.T. / Hansen, S.K. / Romanowski, M.J.
History
DepositionJun 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: serine/threonine kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0522
Polymers31,5491
Non-polymers5021
Water6,648369
1
A: serine/threonine kinase 6
hetero molecules

A: serine/threonine kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1034
Polymers63,0982
Non-polymers1,0052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area4470 Å2
ΔGint-27 kcal/mol
Surface area24370 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.738, 97.738, 62.224
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-408-

HOH

21A-606-

HOH

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Components

#1: Protein serine/threonine kinase 6 / Aurora-A kinase


Mass: 31549.174 Da / Num. of mol.: 1 / Fragment: Aurora A kinase domain, UNP residues 116-382 / Mutation: N186G, K240R, M302L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Aurka, Stk6 / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star Codon+
References: UniProt: Q8C3H8, UniProt: P97477*PLUS, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-AK5 / 3-({3-[(6-amino-5-bromopyrimidin-4-yl)sulfanyl]propanoyl}amino)-4-methoxy-N-phenylbenzamide


Mass: 502.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20BrN5O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.72 Å3/Da / Density % sol: 54.77 %
Crystal growTemperature: 293 K / pH: 5.6
Details: Protein at 8.5 mg/ml in 50 mM Tris pH 7.0, 200 mM NaCl, 3 mM DTT; hanging-drop vapor diffusion; mother liquor: 0.1 M sodium citrate tribasic dihydrate pH 5.6, 2% tacsimate, 16% PEG 3350; ...Details: Protein at 8.5 mg/ml in 50 mM Tris pH 7.0, 200 mM NaCl, 3 mM DTT; hanging-drop vapor diffusion; mother liquor: 0.1 M sodium citrate tribasic dihydrate pH 5.6, 2% tacsimate, 16% PEG 3350; temperature: 293K; cryoprotectant: 20% glycerol; crystal frozen by immersion in liquid nitrogen

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Data collection

DiffractionMean temperature: 160 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 29, 2008 / Details: Vertical focusing mirror
RadiationMonochromator: single crystal (Si111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 32098 / Num. obs: 31664 / % possible obs: 98.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 16.6
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.167 / Mean I/σ(I) obs: 4.9 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQuantumdata collection
CrystalCleardata reduction
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2c6d

2c6d


Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.744 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24299 2449 7.7 %RANDOM
Rwork0.20715 ---
obs0.2099 29178 98.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.476 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20.25 Å20 Å2
2--0.5 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2077 0 31 369 2477
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222160
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1661.9772920
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1525250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.54522.642106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.26615376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5741520
X-RAY DIFFRACTIONr_chiral_restr0.0790.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021647
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.21038
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.21432
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2233
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.275
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6422.51302
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.68252022
X-RAY DIFFRACTIONr_scbond_it3.4652.5994
X-RAY DIFFRACTIONr_scangle_it4.9065898
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.863 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.396 248 -
Rwork0.303 2844 -
obs--99.36 %

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