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- PDB-3uo5: Aurora A in complex with YL1-038-31 -

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Basic information

Entry
Database: PDB / ID: 3uo5
TitleAurora A in complex with YL1-038-31
ComponentsSerine/Threonine-Protein Kinase 6
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / protein kinase / aurora A / inhibitor / DFG-in / 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 / histone H3S10 kinase activity / chromosome passenger complex / positive regulation of oocyte maturation / pronucleus ...Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / histone H3S10 kinase activity / chromosome passenger complex / positive regulation of oocyte maturation / pronucleus / mitotic centrosome separation / meiotic spindle / germinal vesicle / protein localization to centrosome / anterior/posterior axis specification / centrosome localization / spindle organization / neuron projection extension / positive regulation of mitochondrial fission / mitotic spindle pole / SUMOylation of DNA replication proteins / spindle midzone / regulation of G2/M transition of mitotic cell cycle / protein serine/threonine/tyrosine kinase activity / centriole / AURKA Activation by TPX2 / positive regulation of mitotic nuclear division / positive regulation of mitotic cell cycle / mitotic spindle organization / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / ciliary basal body / regulation of cytokinesis / regulation of signal transduction by p53 class mediator / negative regulation of protein binding / 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 / mitotic spindle / kinetochore / response to wounding / spindle / G2/M transition of mitotic cell cycle / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / midbody / peptidyl-serine phosphorylation / basolateral plasma membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / Regulation of TP53 Activity through Phosphorylation / protein autophosphorylation / microtubule / postsynaptic density / non-specific serine/threonine protein kinase / protein kinase activity / protein heterodimerization activity / protein phosphorylation / cell division / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / negative regulation of apoptotic process / 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-0BX / Aurora kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7012 Å
AuthorsMartin, M.P. / Zhu, J.-Y. / Schonbrunn, E.
CitationJournal: Acs Chem.Biol. / Year: 2012
Title: A Novel Mechanism by Which Small Molecule Inhibitors Induce the DFG Flip in Aurora A.
Authors: Martin, M.P. / Zhu, J.Y. / Lawrence, H.R. / Pireddu, R. / Luo, Y. / Alam, R. / Ozcan, S. / Sebti, S.M. / Lawrence, N.J. / Schonbrunn, E.
History
DepositionNov 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1May 2, 2012Group: Database references
Revision 1.2Sep 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

Downloads & links

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Assembly

Deposited unit
A: Serine/Threonine-Protein Kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6652
Polymers32,3591
Non-polymers3061
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.795, 81.795, 173.770
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-A kinase / Serine/threonine kinase 15 / Aurora/IPL1-related kinase 1 / Surora-related kinase ...aurora-A kinase / Serine/threonine kinase 15 / Aurora/IPL1-related kinase 1 / Surora-related kinase 1 / hARK1 / Surora-A / Breast-tumor-amplified kinase /


Mass: 32359.123 Da / Num. of mol.: 1 / Fragment: RESIDUES 123-401 / Mutation: T287D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: AURKA, AIK, AIRK1, ARK1, AURA, AYK1, BTAK, IAK1, STK15, STK6
Plasmid: pET28a-MBP / Production host: Escherichia coli (E. coli) / Strain (production host): TUNER (DE3)
References: UniProt: O14965, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-0BX / 4-{[4-(phenylamino)pyrimidin-2-yl]amino}benzoic acid


Mass: 306.319 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14N4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.6 Å3/Da / Density % sol: 52.67 %
Crystal growTemperature: 291 K / pH: 7.5
Details: 10 mg/mL AURORA A protein, 1 mM YL1-038-31, 10 % (v/v) PEG 3350, 25 mM phosphate(Na/K pH 7.4), 100 mM sodium tartrate pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 8, 2011 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 9540 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rsym value: 0.141 / Net I/σ(I): 36.9
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 7.3 / Rsym value: 0.316 / % possible all: 96.7

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FDN

3fdn


Resolution: 2.7012→19.66 Å / SU ML: 0.37 / σ(F): 0 / Phase error: 25.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2726 416 4.47 %
Rwork0.2174 --
obs0.2199 9314 93.07 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.593 Å2 / ksol: 0.372 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4989 Å2-0 Å20 Å2
2---0.4989 Å2-0 Å2
3---0.9978 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.7012→19.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2194 0 23 39 2256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132349
X-RAY DIFFRACTIONf_angle_d1.2233073
X-RAY DIFFRACTIONf_dihedral_angle_d18.419869
X-RAY DIFFRACTIONf_chiral_restr0.085325
X-RAY DIFFRACTIONf_plane_restr0.005394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7012-3.09070.33061260.25512819X-RAY DIFFRACTION91
3.0907-3.88910.29781430.21092990X-RAY DIFFRACTION95
3.8891-19.66040.23831470.21053089X-RAY DIFFRACTION93

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