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- PDB-2xnn: Structure of Nek2 bound to CCT242430 -

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Basic information

Entry
Database: PDB / ID: 2xnn
TitleStructure of Nek2 bound to CCT242430
ComponentsSERINE/THREONINE-PROTEIN KINASE NEK2
KeywordsTRANSFERASE / CENTROSOME / MITOSIS / CELL CYCLE
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 maintenance / blastocyst development / mitotic spindle assembly / intercellular bridge / spindle assembly ...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 maintenance / blastocyst development / mitotic spindle assembly / intercellular bridge / 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 / APC-Cdc20 mediated degradation of Nek2A / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / condensed nuclear chromosome / meiotic cell cycle / chromosome segregation / kinetochore / spindle pole / Regulation of PLK1 Activity at G2/M Transition / mitotic cell cycle / midbody / protein autophosphorylation / protein phosphatase binding / 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 / non-specific serine/threonine protein kinase / protein kinase activity / ciliary basal body / cilium / protein phosphorylation / cell division / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / nucleolus / protein-containing complex / nucleoplasm / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / 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 domain profile. ...: / 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-430 / Serine/threonine-protein kinase Nek2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMas-Droux, C. / Bayliss, R.
CitationJournal: J.Med.Chem. / Year: 2011
Title: Benzimidazole Inhibitors Induce a Dfg-Out Conformation of Never in Mitosis Gene A-Related Kinase 2 (Nek2) without Binding to the Back Pocket and Reveal a Nonlinear Structure-Activity Relationship.
Authors: Solanki, S. / Innocenti, P. / Mas-Droux, C. / Boxall, K. / Barillari, C. / Van Montfort, R.L. / Aherne, G.W. / Bayliss, R. / Hoelder, S.
History
DepositionAug 5, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 NEK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,64413
Polymers32,6621
Non-polymers98112
Water2,000111
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.210, 56.850, 80.400
Angle α, β, γ (deg.)90.00, 133.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein SERINE/THREONINE-PROTEIN KINASE NEK2 / NEVER IN MITOSIS A-RELATED KINASE 2 / NEK2 / NIMA-RELATED PROTEIN KINASE 2 / NIMA-LIKE PROTEIN ...NEVER IN MITOSIS A-RELATED KINASE 2 / NEK2 / NIMA-RELATED PROTEIN KINASE 2 / NIMA-LIKE PROTEIN KINASE 1 / HSPK 21


Mass: 32662.479 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 1-271
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): RIL
References: UniProt: P51955, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-430 / 5-(1H-benzimidazol-1-yl)-3-{(1R)-1-[2-(trifluoromethyl)phenyl]ethoxy}thiophene-2-carboxamide


Mass: 431.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H16F3N3O2S
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.58 Å3/Da / Density % sol: 52.34 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.5→39.75 Å / Num. obs: 11653 / % possible obs: 99.8 % / Observed criterion σ(I): 6 / Redundancy: 3.2 % / Biso Wilson estimate: 28.56 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.5
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W5A

2w5a


Resolution: 2.5→31.243 Å / SU ML: 0.36 / σ(F): 0.08 / Phase error: 23.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2374 563 5 %
Rwork0.1718 --
obs0.1751 11309 96.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.107 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso mean: 33.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.6882 Å20 Å2-5.4739 Å2
2---6.2392 Å20 Å2
3---7.9274 Å2
Refinement stepCycle: LAST / Resolution: 2.5→31.243 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1986 0 59 111 2156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072090
X-RAY DIFFRACTIONf_angle_d0.9552815
X-RAY DIFFRACTIONf_dihedral_angle_d18.945777
X-RAY DIFFRACTIONf_chiral_restr0.063309
X-RAY DIFFRACTIONf_plane_restr0.005354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.75150.27331190.18612601X-RAY DIFFRACTION94
2.7515-3.14930.26861380.16342664X-RAY DIFFRACTION97
3.1493-3.96660.19811530.14782700X-RAY DIFFRACTION98
3.9666-31.24510.23771530.17842781X-RAY DIFFRACTION98

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