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- PDB-3ha6: Crystal structure of aurora A in complex with TPX2 and compound 10 -

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Basic information

Entry
Database: PDB / ID: 3ha6
TitleCrystal structure of aurora A in complex with TPX2 and compound 10
Components
  • Serine/threonine-protein kinase 6
  • Targeting protein for Xklp2
KeywordsTRANSFERASE / AURORA A / SERINE/THREONINE-PROTEIN KINASE / COFACTOR / TPX2 / INHIBITOR / PHOSPHORYLATION / ATP-BINDING / CELL CYCLE / NUCLEOTIDE-BINDING / PHOSPHOPROTEIN / NUCLEUS / Kinase
Function / homology
Function and homology information


importin-alpha family protein binding / Interaction between PHLDA1 and AURKA / activation of protein kinase activity / regulation of centrosome cycle / negative regulation of microtubule depolymerization / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / chromosome passenger complex ...importin-alpha family protein binding / Interaction between PHLDA1 and AURKA / activation of protein kinase activity / regulation of centrosome cycle / negative regulation of microtubule depolymerization / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / chromosome passenger complex / microtubule nucleation / 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 / mitotic spindle assembly / spindle midzone / intercellular bridge / 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 / regulation of mitotic spindle organization / 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 / molecular adaptor activity / 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
Similarity search - Function
TPX2 / Aurora-A binding / TPX2, C-terminal / TPX2 central domain / Targeting protein for Xklp2 (TPX2) domain / Aurora-A binding / Cell cycle regulated microtubule associated protein / Aurora kinase A / Aurora kinase / Phosphorylase Kinase; domain 1 ...TPX2 / Aurora-A binding / TPX2, C-terminal / TPX2 central domain / Targeting protein for Xklp2 (TPX2) domain / Aurora-A binding / Cell cycle regulated microtubule associated protein / 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-2JZ / Aurora kinase A / Targeting protein for Xklp2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsZhao, B. / Clark, M.A.
CitationJournal: Nat.Chem.Biol. / Year: 2009
Title: Design, synthesis and selection of DNA-encoded small-molecule libraries.
Authors: Clark, M.A. / Acharya, R.A. / Arico-Muendel, C.C. / Belyanskaya, S.L. / Benjamin, D.R. / Carlson, N.R. / Centrella, P.A. / Chiu, C.H. / Creaser, S.P. / Cuozzo, J.W. / Davie, C.P. / Ding, Y. ...Authors: Clark, M.A. / Acharya, R.A. / Arico-Muendel, C.C. / Belyanskaya, S.L. / Benjamin, D.R. / Carlson, N.R. / Centrella, P.A. / Chiu, C.H. / Creaser, S.P. / Cuozzo, J.W. / Davie, C.P. / Ding, Y. / Franklin, G.J. / Franzen, K.D. / Gefter, M.L. / Hale, S.P. / Hansen, N.J. / Israel, D.I. / Jiang, J. / Kavarana, M.J. / Kelley, M.S. / Kollmann, C.S. / Li, F. / Lind, K. / Mataruse, S. / Medeiros, P.F. / Messer, J.A. / Myers, P. / O'Keefe, H. / Oliff, M.C. / Rise, C.E. / Satz, A.L. / Skinner, S.R. / Svendsen, J.L. / Tang, L. / van Vloten, K. / Wagner, R.W. / Yao, G. / Zhao, B. / Morgan, B.A.
History
DepositionMay 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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
B: Targeting protein for Xklp2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7493
Polymers36,2382
Non-polymers5121
Water52229
1
A: Serine/threonine-protein kinase 6
B: Targeting protein for Xklp2
hetero molecules

A: Serine/threonine-protein kinase 6
B: Targeting protein for Xklp2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4996
Polymers72,4764
Non-polymers1,0232
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area8980 Å2
ΔGint-46 kcal/mol
Surface area26100 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-15 kcal/mol
Surface area14750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.464, 86.464, 143.345
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 31253.707 Da / Num. of mol.: 1 / Fragment: UNP residues 125-391
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AIK, ARK1, AURA, AURKA, BTAK, STK15, STK6 / Plasmid: PDEST17 TEV AURORA A 125-391 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: O14965, non-specific serine/threonine protein kinase
#2: Protein/peptide Targeting protein for Xklp2 / Restricted expression proliferation-associated protein 100 / p100 / Differentially expressed in ...Restricted expression proliferation-associated protein 100 / p100 / Differentially expressed in cancerous and non-cancerous lung cells 2 / DIL-2 / Protein fls353 / Hepatocellular carcinoma-associated antigen 519


Mass: 4984.162 Da / Num. of mol.: 1 / Fragment: UNP residues 1-43
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C20orf1, C20orf2, DIL2, HCA519, TPX2 / Plasmid: PDEST17 TEV AURORA A 125-391 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9ULW0
#3: Chemical ChemComp-2JZ / N~2~-(3,4-dimethoxyphenyl)-N~4~-[2-(2-fluorophenyl)ethyl]-N~6~-quinolin-6-yl-1,3,5-triazine-2,4,6-triamine


Mass: 511.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H26FN7O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.27 Å3/Da / Density % sol: 71.18 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.36→50 Å / Num. obs: 22350 / % possible obs: 84 % / Observed criterion σ(I): 2

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.36→25 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.925 / SU B: 16.787 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.305 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25242 1215 5.9 %RANDOM
Rwork0.22382 ---
obs0.2254 19335 78.69 %-
all-22350 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 62.454 Å2
Baniso -1Baniso -2Baniso -3
1-4.68 Å22.34 Å20 Å2
2--4.68 Å20 Å2
3----7.01 Å2
Refinement stepCycle: LAST / Resolution: 2.36→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2458 0 38 29 2525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222557
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1731.9853452
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2225295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.89622.951122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.67915438
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6441521
X-RAY DIFFRACTIONr_chiral_restr0.0670.2362
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022000
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.21171
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21719
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2102
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2780.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3881.51539
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.42222402
X-RAY DIFFRACTIONr_scbond_it0.81331181
X-RAY DIFFRACTIONr_scangle_it1.0754.51050
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.36→2.421 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 37 -
Rwork0.359 613 -
obs--34.83 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.03460.85711.10674.01650.25473.55840.0494-0.0899-0.0635-0.0193-0.09680.37750.4697-0.33080.0474-0.1665-0.1804-0.055-0.0675-0.0325-0.0673-36.324223.812117.5029
22.0220.7306-0.86793.63230.5816.258-0.23170.01950.0374-0.51710.08710.23470.1875-0.52120.1446-0.1105-0.1403-0.1781-0.1841-0.0165-0.0831-32.500734.34940.9939
33.04712.3285-1.52692.84941.14135.7440.2441-0.71770.767-0.2168-0.18830.1457-0.4548-0.5526-0.0559-0.1132-0.0759-0.1734-0.1843-0.0759-0.0653-25.124243.774715.9502
43.43590.3661-0.43872.3764-0.01645.4105-0.14380.24830.4513-0.45890.0280.0992-0.3504-0.08730.11580.0634-0.1014-0.1463-0.33980.059-0.0912-22.231745.3287-1.2071
53.036-1.03870.36222.37281.95492.6275-0.4499-0.10530.3058-0.0921-0.12660.51610.7761-0.39820.5765-0.199-0.3027-0.0008-0.0207-0.04430.1188-37.777528.342825.2746
68.58760.0112-1.989530.547114.24679.5266-1.22191.07231.1276-0.33041.48470.8788-2.308-0.0465-0.26280.18840.0517-0.02780.3928-0.03360.4653-43.331844.584621.6924
713.1019-13.1905-10.212334.8541-5.959868.7253-0.81320.2512-1.8837-0.56631.2045-2.30450.48681.214-0.39140.2906-0.4058-0.043-0.1007-0.02560.211-29.195723.11156.386
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A124 - 212
2X-RAY DIFFRACTION2A213 - 276
3X-RAY DIFFRACTION3A277 - 294
4X-RAY DIFFRACTION4A295 - 388
5X-RAY DIFFRACTION5B0 - 23
6X-RAY DIFFRACTION6B30 - 42
7X-RAY DIFFRACTION7A1

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