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- PDB-3qbn: Structure of Human Aurora A in Complex with a diaminopyrimidine -

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Basic information

Entry
Database: PDB / ID: 3qbn
TitleStructure of Human Aurora A in Complex with a diaminopyrimidine
ComponentsSerine/threonine-protein kinase 6
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Kinase Domain / Diaminopyrimidine / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 / chromosome passenger complex / positive regulation of oocyte maturation / pronucleus / mitotic centrosome separation ...Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / chromosome passenger complex / positive regulation of oocyte maturation / pronucleus / mitotic centrosome separation / germinal vesicle / meiotic spindle / protein localization to centrosome / anterior/posterior axis specification / centrosome localization / neuron projection extension / spindle organization / positive regulation of mitochondrial fission / mitotic spindle pole / SUMOylation of DNA replication proteins / spindle midzone / regulation of G2/M transition of mitotic cell cycle / negative regulation of protein binding / centriole / protein serine/threonine/tyrosine kinase activity / positive regulation of mitotic nuclear division / positive regulation of mitotic cell cycle / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / molecular function activator activity / AURKA Activation by TPX2 / liver regeneration / regulation of cytokinesis / regulation of signal transduction by p53 class mediator / mitotic spindle organization / 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 / kinetochore / response to wounding / spindle / spindle pole / G2/M transition of mitotic cell cycle / mitotic spindle / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / peptidyl-serine phosphorylation / microtubule cytoskeleton / midbody / protein autophosphorylation / basolateral plasma membrane / Regulation of TP53 Activity through Phosphorylation / microtubule / proteasome-mediated ubiquitin-dependent protein catabolic process / 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 kinase activity / postsynaptic density / ciliary basal body / protein phosphorylation / protein heterodimerization activity / cell division / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / centrosome / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Aurora kinase A / 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 ...Aurora kinase A / 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-E9Z / Aurora kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å
AuthorsGruetter, C. / Simard, J.R. / Rauh, D.
CitationJournal: Acs Chem.Biol. / Year: 2011
Title: Identification of Ustilago maydis Aurora kinase as a novel antifungal target.
Authors: Tueckmantel, S. / Greul, J.N. / Janning, P. / Brockmeyer, A. / Gruetter, C. / Simard, J.R. / Gutbrod, O. / Beck, M.E. / Tietjen, K. / Rauh, D. / Schreier, P.H.
History
DepositionJan 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8372
Polymers32,5021
Non-polymers3351
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.200, 84.200, 169.330
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Serine/threonine-protein kinase 6 / Aurora kinase A / Aurora/IPL1-related kinase 1 / ARK-1 / Aurora-related kinase 1 / hARK1 / Breast ...Aurora kinase A / Aurora/IPL1-related kinase 1 / ARK-1 / Aurora-related kinase 1 / hARK1 / Breast tumor-amplified kinase / Serine/threonine-protein kinase 15 / Serine/threonine-protein kinase aurora-A


Mass: 32502.205 Da / Num. of mol.: 1 / Fragment: unp residues 124-403 / Mutation: V279C, C290S, C393S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AURKA, AIK, ARK1, AURA, BTAK, STK15, STK6 / Plasmid: pET 28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O14965, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-E9Z / 5-chloro-N~4~-cyclopropyl-N~2~-[4-(2-methoxyethoxy)phenyl]pyrimidine-2,4-diamine


Mass: 334.801 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19ClN4O2

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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: 2.67 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 100 mM Na-citrate, 15-20% PEG8000, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9786 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2010 / Details: Dynamic bendable mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 3.5→45 Å / Num. all: 4902 / Num. obs: 4883 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 112.241 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 27.27
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
3.5-3.65.50.6722.72025369369100
3.6-3.70.3974.41938343100
3.7-40.2327.4456684199.9
4-4.50.08118.6514694899.8
4.5-70.03834.48787170299.6
7-120.01568.5250753099.8
12-160.01481.33288397.6
160.0177.92226791.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 39.44 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å42.1 Å
Translation3.5 Å42.1 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2DWB

2dwb


Resolution: 3.5→40 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.89 / WRfactor Rfree: 0.3115 / WRfactor Rwork: 0.2253 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6987 / SU B: 50.979 / SU ML: 0.752 / SU Rfree: 0.869 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.869 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3336 732 15 %RANDOM
Rwork0.2436 ---
obs0.2573 4881 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 173.64 Å2 / Biso mean: 131.898 Å2 / Biso min: 95.68 Å2
Baniso -1Baniso -2Baniso -3
1--2.33 Å2-1.17 Å20 Å2
2---2.33 Å20 Å2
3---3.5 Å2
Refinement stepCycle: LAST / Resolution: 3.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2038 0 23 0 2061
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222112
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.9852856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4115248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86223.039102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.56815368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5671518
X-RAY DIFFRACTIONr_chiral_restr0.1020.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211604
X-RAY DIFFRACTIONr_mcbond_it0.6911.51247
X-RAY DIFFRACTIONr_mcangle_it1.28222008
X-RAY DIFFRACTIONr_scbond_it1.0263865
X-RAY DIFFRACTIONr_scangle_it1.8454.5845
LS refinement shellResolution: 3.5→3.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.473 50 -
Rwork0.318 283 -
all-333 -
obs--100 %

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