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- PDB-5m57: Nek2 bound to arylaminopurine 6 -

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Basic information

Entry
Database: PDB / ID: 5m57
TitleNek2 bound to arylaminopurine 6
ComponentsSerine/threonine-protein kinase Nek2
KeywordsTRANSFERASE / Protein kinase / inhibitor / centrosome separation
Function / homology
Function and homology information


negative regulation of centriole-centriole cohesion / centrosome separation / regulation of attachment of spindle microtubules to kinetochore / regulation of mitotic centrosome separation / regulation of mitotic nuclear division / positive regulation of telomere capping / mitotic spindle assembly / blastocyst development / spindle assembly / Loss of Nlp from mitotic centrosomes ...negative regulation of centriole-centriole cohesion / centrosome separation / regulation of attachment of spindle microtubules to kinetochore / regulation of mitotic centrosome separation / regulation of mitotic nuclear division / positive regulation of telomere capping / mitotic spindle assembly / blastocyst development / spindle assembly / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / positive regulation of telomerase activity / positive regulation of telomere maintenance via telomerase / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / APC-Cdc20 mediated degradation of Nek2A / AURKA Activation by TPX2 / meiotic cell cycle / condensed nuclear chromosome / chromosome segregation / kinetochore / spindle pole / Regulation of PLK1 Activity at G2/M Transition / mitotic cell cycle / midbody / protein phosphatase binding / microtubule / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / cell division / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / nucleolus / protein-containing complex / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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 domain profile. / Protein kinase domain ...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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-4SP / Serine/threonine-protein kinase Nek2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBayliss, R.
CitationJournal: Oncotarget / Year: 2017
Title: Structure-guided design of purine-based probes for selective Nek2 inhibition.
Authors: Coxon, C.R. / Wong, C. / Bayliss, R. / Boxall, K. / Carr, K.H. / Fry, A.M. / Hardcastle, I.R. / Matheson, C.J. / Newell, D.R. / Sivaprakasam, M. / Thomas, H. / Turner, D. / Yeoh, S. / Wang, ...Authors: Coxon, C.R. / Wong, C. / Bayliss, R. / Boxall, K. / Carr, K.H. / Fry, A.M. / Hardcastle, I.R. / Matheson, C.J. / Newell, D.R. / Sivaprakasam, M. / Thomas, H. / Turner, D. / Yeoh, S. / Wang, L.Z. / Griffin, R.J. / Golding, B.T. / Cano, C.
History
DepositionOct 20, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Jan 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:
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Assembly

Deposited unit
A: Serine/threonine-protein kinase Nek2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0352
Polymers32,6321
Non-polymers4021
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-2 kcal/mol
Surface area13700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.733, 73.595, 75.393
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Serine/threonine-protein kinase Nek2 / HSPK 21 / Never in mitosis A-related kinase 2 / NimA-related protein kinase 2 / NimA-like protein kinase 1


Mass: 32632.451 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEK2, NEK2A, NLK1 / Production host: Escherichia coli (E. coli)
References: UniProt: P51955, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-4SP / O6-CYCLOHEXYLMETHOXY-2-(4'-SULPHAMOYLANILINO) PURINE


Mass: 402.471 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22N6O3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 3 % PEG 8000, 50 mM Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 12, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.3→73.5 Å / Num. obs: 14309 / % possible obs: 98.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 13.6
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 3.1 / % possible all: 90.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W5A
Resolution: 2.3→52.664 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2742 704 4.93 %
Rwork0.2186 --
obs0.2213 14267 98.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→52.664 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2065 0 28 40 2133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092139
X-RAY DIFFRACTIONf_angle_d1.2362899
X-RAY DIFFRACTIONf_dihedral_angle_d16.419787
X-RAY DIFFRACTIONf_chiral_restr0.048318
X-RAY DIFFRACTIONf_plane_restr0.005369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.47760.30041380.24632477X-RAY DIFFRACTION92
2.4776-2.72690.29021450.23772725X-RAY DIFFRACTION100
2.7269-3.12150.27591320.23462734X-RAY DIFFRACTION100
3.1215-3.93250.29451310.22012786X-RAY DIFFRACTION100
3.9325-52.67740.25411580.20392841X-RAY DIFFRACTION98

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