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- PDB-6s75: Crystal structure of Nek7 bound to compound 51 -

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Basic information

Entry
Database: PDB / ID: 6s75
TitleCrystal structure of Nek7 bound to compound 51
ComponentsSerine/threonine-protein kinase Nek7
KeywordsCELL CYCLE / Kinase / inhibitor
Function / homology
Function and homology information


NEK6-subfamily protein kinase / Activation of NIMA Kinases NEK9, NEK6, NEK7 / Nuclear Pore Complex (NPC) Disassembly / cellular response to potassium ion / positive regulation of NLRP3 inflammasome complex assembly / positive regulation of telomere maintenance / microtubule organizing center / spindle assembly / EML4 and NUDC in mitotic spindle formation / positive regulation of telomere maintenance via telomerase ...NEK6-subfamily protein kinase / Activation of NIMA Kinases NEK9, NEK6, NEK7 / Nuclear Pore Complex (NPC) Disassembly / cellular response to potassium ion / positive regulation of NLRP3 inflammasome complex assembly / positive regulation of telomere maintenance / microtubule organizing center / spindle assembly / EML4 and NUDC in mitotic spindle formation / positive regulation of telomere maintenance via telomerase / regulation of mitotic cell cycle / molecular function activator activity / spindle pole / microtubule / 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 / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Serine-threonine/tyrosine-protein kinase, catalytic domain / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...Serine-threonine/tyrosine-protein kinase, catalytic domain / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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-F9N / Serine/threonine-protein kinase Nek7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsNasir, N. / Bayliss, R.
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
DepositionJul 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase Nek7
B: Serine/threonine-protein kinase Nek7
C: Serine/threonine-protein kinase Nek7
D: Serine/threonine-protein kinase Nek7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,1437
Polymers142,6804
Non-polymers1,4633
Water00
1
A: Serine/threonine-protein kinase Nek7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1582
Polymers35,6701
Non-polymers4881
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase Nek7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1582
Polymers35,6701
Non-polymers4881
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Serine/threonine-protein kinase Nek7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1582
Polymers35,6701
Non-polymers4881
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Serine/threonine-protein kinase Nek7


Theoretical massNumber of molelcules
Total (without water)35,6701
Polymers35,6701
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.405, 168.971, 84.565
Angle α, β, γ (deg.)90.000, 90.029, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Serine/threonine-protein kinase Nek7 / Never in mitosis A-related kinase 7 / NimA-related protein kinase 7


Mass: 35670.113 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEK7 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8TDX7, 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.: 3 / Source method: obtained synthetically / Formula: C23H33N7O3S / Feature type: SUBJECT OF INVESTIGATION
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: 2.52 Å3/Da / Density % sol: 51.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20 % w/v Polyethylene glycol 3,350, 150 mM di-Sodium DL-malate; pH 7.0, 3% w/v 1,6-Hexanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 3.3→75.62 Å / Num. obs: 21271 / % possible obs: 96.45 % / Redundancy: 6.6 % / Biso Wilson estimate: 63.04 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Net I/σ(I): 15.28
Reflection shellResolution: 3.3→3.42 Å / Num. unique obs: 1700

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
autoPROCdata scaling
PHENIX1.14_3260phasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GT1

6gt1
PDB Unreleased entry


Resolution: 3.3→75.62 Å / SU ML: 0.5266 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.4574
RfactorNum. reflection% reflection
Rfree0.3169 1006 4.9 %
Rwork0.2602 --
obs0.2629 20549 96.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 49.42 Å2
Refinement stepCycle: LAST / Resolution: 3.3→75.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7615 0 102 0 7717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00257904
X-RAY DIFFRACTIONf_angle_d0.551610797
X-RAY DIFFRACTIONf_chiral_restr0.04021216
X-RAY DIFFRACTIONf_plane_restr0.00341394
X-RAY DIFFRACTIONf_dihedral_angle_d5.73884697
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.470.37731290.32372325X-RAY DIFFRACTION81.64
3.47-3.690.34271330.29732780X-RAY DIFFRACTION94.7
3.69-3.980.3371220.28362894X-RAY DIFFRACTION99.97
3.98-4.380.31611280.2492889X-RAY DIFFRACTION99.9
4.38-5.010.32711630.23882908X-RAY DIFFRACTION99.97
5.01-6.310.31761830.26922867X-RAY DIFFRACTION99.84
6.31-75.620.26681480.22832880X-RAY DIFFRACTION98.99

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