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- PDB-3uo6: Aurora A in complex with YL5-083 -

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Basic information

Entry
Database: PDB / ID: 3uo6
TitleAurora A in complex with YL5-083
ComponentsAurora kinase A
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / protein kinase / aurora A / inhibitor / DFG-out / 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 / 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-0BY / Aurora kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8002 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

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Assembly

Deposited unit
A: Aurora kinase A
B: Aurora kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6488
Polymers64,7182
Non-polymers9306
Water37821
1
A: Aurora kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8244
Polymers32,3591
Non-polymers4653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aurora kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8244
Polymers32,3591
Non-polymers4653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-14 kcal/mol
Surface area25000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.700, 85.700, 76.650
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 126:389 )
211chain B and (resseq 126:389 )

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Components

#1: Protein Aurora kinase A / / Aurora 2 / Aurora/IPL1-related kinase 1 / ARK-1 / Aurora-related kinase 1 / hARK1 / Breast tumor- ...Aurora 2 / 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 6 / Serine/threonine-protein kinase aurora-A


Mass: 32359.123 Da / Num. of mol.: 2 / Fragment: Kinase domain 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-0BY / 4-({4-[(2-chlorophenyl)amino]pyrimidin-2-yl}amino)benzoic acid


Mass: 340.764 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H13ClN4O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.51 Å3/Da / Density % sol: 51.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10 mg/mL AURORA A protein, 1 mM YL5-083, 10 % (v/v) PEG 3350, 25 mM phosphate(Na/K pH 7.4), 5 % Tacismate 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 / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 4, 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: 2.8→20 Å / Num. obs: 15369 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.068 / Rsym value: 0.039 / Net I/σ(I): 31.79
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 4.7 / Rsym value: 0.315 / % possible all: 99.7

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3UNZ

3unz


Resolution: 2.8002→18.889 Å / SU ML: 0.41 / σ(F): 2 / Phase error: 29.96 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.2764 614 4 %
Rwork0.2287 --
obs-15345 99.26 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.717 Å2 / ksol: 0.319 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.9091 Å2-0 Å2-0 Å2
2--0.9091 Å20 Å2
3----1.8183 Å2
Refine analyze
FreeObs
Luzzati sigma a0.54 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.8002→18.889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4338 0 64 21 4423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134512
X-RAY DIFFRACTIONf_angle_d1.4626090
X-RAY DIFFRACTIONf_dihedral_angle_d20.841714
X-RAY DIFFRACTIONf_chiral_restr0.089644
X-RAY DIFFRACTIONf_plane_restr0.007780
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2170X-RAY DIFFRACTIONPOSITIONAL
12B2170X-RAY DIFFRACTIONPOSITIONAL0.112
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8002-3.08090.41991540.34943714X-RAY DIFFRACTION100
3.0809-3.52420.32591530.27083660X-RAY DIFFRACTION100
3.5242-4.43070.26411540.20083709X-RAY DIFFRACTION99
4.4307-18.88970.20981530.18593648X-RAY DIFFRACTION99

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