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- PDB-6gra: Human AURKA bound to BRD-7880 -

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Basic information

Entry
Database: PDB / ID: 6gra
TitleHuman AURKA bound to BRD-7880
ComponentsAurora kinase A
KeywordsTRANSFERASE / Kinase / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / cilium disassembly / spindle pole centrosome / mitotic centrosome separation / histone H3S10 kinase activity / chromosome passenger complex / pronucleus / regulation of G2/M transition of mitotic cell cycle ...Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / cilium disassembly / spindle pole centrosome / mitotic centrosome separation / histone H3S10 kinase activity / chromosome passenger complex / pronucleus / regulation of G2/M transition of mitotic cell cycle / germinal vesicle / meiotic spindle organization / meiotic spindle / spindle organization / positive regulation of mitochondrial fission / mitotic spindle pole / spindle midzone / SUMOylation of DNA replication proteins / negative regulation of protein binding / positive regulation of mitotic cell cycle / positive regulation of mitotic nuclear division / protein serine/threonine/tyrosine kinase activity / centriole / liver regeneration / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / AURKA Activation by TPX2 / regulation of signal transduction by p53 class mediator / molecular function activator activity / mitotic spindle organization / regulation of cytokinesis / G2/M transition of mitotic cell cycle / response to wounding / regulation of protein stability / peptidyl-serine phosphorylation / 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 / spindle / kinetochore / spindle pole / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / protein autophosphorylation / mitotic cell cycle / ciliary basal body / midbody / Regulation of TP53 Activity through Phosphorylation / basolateral plasma membrane / microtubule / protein kinase activity / protein phosphorylation / non-specific serine/threonine protein kinase / postsynaptic density / protein heterodimerization activity / negative regulation of gene expression / protein serine kinase activity / cell division / ubiquitin protein ligase binding / protein serine/threonine kinase activity / centrosome / 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-F8Z / Aurora kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsAbdul Azeez, K.R. / Sorrell, F.J. / von Delft, F. / Bountra, C. / Knapp, S. / Edwards, A.M. / Arrowsmith, C. / Elkins, J.M.
CitationJournal: To Be Published
Title: Aurora kinase A bound to BRD-7880
Authors: Abdul Azeez, K.R. / Elkins, J.M.
History
DepositionJun 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aurora kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5392
Polymers32,9491
Non-polymers5911
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.169, 83.169, 171.852
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-603-

HOH

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Components

#1: Protein Aurora kinase A / Aurora 2 / Aurora/IPL1-related kinase 1 / hARK1 / Breast tumor-amplified kinase / Serine/threonine- ...Aurora 2 / Aurora/IPL1-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: 32948.781 Da / Num. of mol.: 1
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
Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli)
References: UniProt: O14965, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-F8Z / 1-[(2~{R},3~{S})-2-[[1,3-benzodioxol-5-ylmethyl(methyl)amino]methyl]-3-methyl-6-oxidanylidene-5-[(2~{S})-1-oxidanylpropan-2-yl]-3,4-dihydro-2~{H}-1,5-benzoxazocin-8-yl]-3-(4-methoxyphenyl)urea


Mass: 590.667 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H38N4O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 52.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M potassium citrate, 0.1 M Bis-Tris propane pH 7.5, 20% PEG 3350, 10% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Sep 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.6→85.93 Å / Num. obs: 11497 / % possible obs: 100 % / Redundancy: 8.6 % / CC1/2: 0.999 / Rsym value: 0.07 / Net I/σ(I): 13.3
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1603 / CC1/2: 0.818 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J4Z

2j4z


Resolution: 2.6→66.52 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.915 / SU B: 25.51 / SU ML: 0.251 / Cross valid method: THROUGHOUT / ESU R: 0.473 / ESU R Free: 0.306 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26859 548 4.8 %RANDOM
Rwork0.21005 ---
obs0.21277 10877 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 75.206 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å2-0.47 Å2-0 Å2
2---0.94 Å2-0 Å2
3---3.05 Å2
Refinement stepCycle: 1 / Resolution: 2.6→66.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1976 0 43 3 2022
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0142071
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171867
X-RAY DIFFRACTIONr_angle_refined_deg1.2911.6512810
X-RAY DIFFRACTIONr_angle_other_deg0.8351.6264343
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8655248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.03521.553103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.65615339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8251512
X-RAY DIFFRACTIONr_chiral_restr0.2690.2262
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022302
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02402
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.794.684998
X-RAY DIFFRACTIONr_mcbond_other1.7874.68997
X-RAY DIFFRACTIONr_mcangle_it2.8467.0211244
X-RAY DIFFRACTIONr_mcangle_other2.8477.0261245
X-RAY DIFFRACTIONr_scbond_it2.0765.021073
X-RAY DIFFRACTIONr_scbond_other2.0765.0211074
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2737.4431567
X-RAY DIFFRACTIONr_long_range_B_refined4.76954.842260
X-RAY DIFFRACTIONr_long_range_B_other4.76954.8362261
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.509 32 -
Rwork0.353 774 -
obs--99.63 %
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)
16.4161.2736-1.46473.01011.84154.3289-0.09680.2188-1.1117-0.03280.02140.06961.0809-0.19860.07540.5395-0.112-0.07820.2362-0.0360.4802-0.095422.7933-11.2578
29.20131.8121-1.245523.1934-7.293311.66190.16380.19710.31310.01920.01550.87230.031-0.4673-0.17930.4254-0.09450.03740.4667-0.1070.4873-15.562422.1339-18.7242
36.4374-1.4562-1.89032.77421.13982.4809-0.10760.4805-0.1480.01870.1419-0.09610.2452-0.1718-0.03430.2604-0.133-0.03510.23810.07680.1051-12.465734.8483-9.9043
43.83531.7162-2.36897.53533.181513.0693-0.4720.5046-0.7666-0.71240.14150.05021.0054-0.17870.33050.3573-0.1001-0.0060.3586-0.06770.2995-28.611727.471-4.406
55.0422-0.572-1.67494.6431-0.48453.8097-0.17240.59420.4729-0.05480.08190.376-0.2003-0.55890.09050.151-0.0133-0.04230.22210.04250.1221-29.208340.2598-1.8422
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A126 - 173
2X-RAY DIFFRACTION2A174 - 188
3X-RAY DIFFRACTION3A189 - 273
4X-RAY DIFFRACTION4A274 - 305
5X-RAY DIFFRACTION5A306 - 388

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