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- PDB-6sk9: Nek2 bound to purine compound 51 -

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Basic information

Entry
Database: PDB / ID: 6sk9
TitleNek2 bound to purine compound 51
ComponentsSerine/threonine-protein kinase Nek2
KeywordsTRANSFERASE / Ser/Thr protein kinase
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 / blastocyst development / mitotic spindle assembly / 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 / blastocyst development / mitotic spindle assembly / 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 / Recruitment of NuMA to mitotic centrosomes / positive regulation of telomere maintenance via telomerase / 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
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 / Alpha Beta
Similarity search - Domain/homology
Chem-F9N / Serine/threonine-protein kinase Nek2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBayliss, R. / Byrne, M.J. / Mas-Droux, C.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Cancer Research UKC24461/ A13231 United Kingdom
Medical Research Council (United Kingdom)MR/L017032/1 United Kingdom
CitationJournal: Biochem.J. / Year: 2020
Title: Nek7 conformational flexibility and inhibitor binding probed through protein engineering of the R-spine.
Authors: Byrne, M.J. / Nasir, N. / Basmadjian, C. / Bhatia, C. / Cunnison, R.F. / Carr, K.H. / Mas-Droux, C. / Yeoh, S. / Cano, C. / Bayliss, R.
History
DepositionAug 15, 2019Deposition site: PDBE / Processing site: PDBE
SupersessionJun 17, 2020ID: 6H0O
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,2423
Polymers32,6621
Non-polymers5802
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-0 kcal/mol
Surface area12820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.02, 56.89, 77.94
Angle α, β, γ (deg.)90.0, 132.42, 90.0
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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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: 32662.479 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-F9N / 3-[[6-(cyclohexylmethoxy)-7~{H}-purin-2-yl]amino]-~{N}-[3-(dimethylamino)propyl]benzenesulfonamide


Mass: 487.618 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H33N7O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.88 Å3/Da / Density % sol: 57.33 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop
Details: 50 mM Hepes, pH 7.5, 300 mM sodium chloride, 10 mM sodium phosphate, 5 mM dithiothreitol and 5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→30.63 Å / Num. obs: 21992 / % possible obs: 99.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 31.3770207207 Å2 / CC1/2: 0.997 / Net I/σ(I): 8.5
Reflection shellResolution: 2→2.11 Å / Num. unique obs: 3167 / CC1/2: 0.679

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30.63 Å / SU ML: 0.186498588615 / Cross valid method: FREE R-VALUE / σ(F): 1.35040804944 / Phase error: 23.177789498
RfactorNum. reflection% reflection
Rfree0.219599199899 1112 5.09437419828 %
Rwork0.187889564471 --
obs0.189516994103 21828 99.272330362 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 49.6367037345 Å2
Refinement stepCycle: LAST / Resolution: 2→30.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1894 0 40 91 2025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008043931607121981
X-RAY DIFFRACTIONf_angle_d1.029291176582680
X-RAY DIFFRACTIONf_chiral_restr0.0408423445935294
X-RAY DIFFRACTIONf_plane_restr0.00463971770443338
X-RAY DIFFRACTIONf_dihedral_angle_d16.432334505730
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0910.321884340031320.2490261257352572X-RAY DIFFRACTION99.7417926964
2.091-2.20120.2273971069641410.2114107893992601X-RAY DIFFRACTION99.8543335761
2.2012-2.33910.2371447170251550.1840147943222551X-RAY DIFFRACTION99.9630587366
2.3391-2.51960.1923077940751390.1737136498892612X-RAY DIFFRACTION99.9273519797
2.5196-2.7730.200663192491240.1833279659512608X-RAY DIFFRACTION99.780861943
2.773-3.1740.2255871816871360.1796230326582595X-RAY DIFFRACTION99.5625227853
3.174-3.99750.2027961644661480.1754200685362600X-RAY DIFFRACTION99.3851717902
3.9975-30.630.2257451586591370.1936603023692577X-RAY DIFFRACTION96.1388593695
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)
10.145687895249-0.254252203258-0.1770548506540.3623913706830.2975667742240.218656486017-0.5681184299160.539844608836-0.189262739243-0.3822498397210.1730924584420.3036032523180.08381660410760.08519361661780.2538498977051.08014539247-0.165101612832-0.1388856184251.06887217215-0.1724889277640.918150127625-20.59013814743.13010828931-2.37252781501
23.749382999611.590819048660.8693248722442.691371530890.4524738953791.28595946849-0.09408649859050.3478011931750.0305508744139-0.310877393236-0.01616740230210.06329259303820.016589928777-0.2976505987270.1106229749360.233586743801-0.001431088824260.01704005827410.295433047044-0.01597791698750.196507575778-16.02010893869.8137440295817.9139890879
31.745028574280.63118341781-0.2394890080662.874622625450.3324195501592.31806001935-0.1448601848920.1983302910050.0571780433061-0.2030097340360.0712426020233-0.151533697016-0.1838656615780.006164432668760.07131496348850.235408737689-0.0225736552152-0.01012254927960.204245114033-0.0128550105430.243425169919-4.0530677182920.508970265521.6880768725
42.04817243827-0.09628268372410.0718606533412.07148950144-0.1194839916593.7885956441-0.05270997067910.612347106647-0.434912672059-0.5143729146710.1691322689510.4530544811760.107012257275-0.194817805864-0.01061883870960.298237327282-0.0783946212133-0.04646598684240.440195496832-0.07257122213660.39941541272-31.77671745330.60659627696713.1715745637
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 45 through 59 )
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 194 )
3X-RAY DIFFRACTION3chain 'A' and (resid 195 through 279 )
4X-RAY DIFFRACTION4chain 'A' and (resid 4 through 44)

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