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- PDB-2xnm: Structure of NEK2 bound to CCT -

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Basic information

Entry
Database: PDB / ID: 2xnm
TitleStructure of NEK2 bound to CCT
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 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 / Anchoring of the basal body to the plasma membrane / positive regulation of telomere maintenance via telomerase / 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-WGZ / Serine/threonine-protein kinase Nek2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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

Downloads & links

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Assembly

Deposited unit
A: SERINE/THREONINE-PROTEIN KINASE NEK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,93214
Polymers32,6621
Non-polymers1,27013
Water4,684260
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.800, 56.830, 81.300
Angle α, β, γ (deg.)90.00, 133.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#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)
References: UniProt: P51955, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 273 molecules

#2: Chemical ChemComp-WGZ / 5-{6-[(1-METHYLPIPERIDIN-4-YL)OXY]-1H-BENZIMIDAZOL-1-YL}-3-{(1R)-1-[2-(TRIFLUOROMETHYL)PHENYL]ETHOXY}THIOPHENE-2-CARBOXAMIDE


Mass: 544.588 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H27F3N4O3S
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 52.66 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.79→46.17 Å / Num. obs: 27237 / % possible obs: 98.1 % / Observed criterion σ(I): 6 / Redundancy: 2.6 % / Biso Wilson estimate: 18.54 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.1
Reflection shellResolution: 1.79→1.89 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.5 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→36.734 Å / SU ML: 0.21 / σ(F): 0.02 / Phase error: 17.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1962 1391 5.1 %
Rwork0.1632 --
obs0.1649 27237 94.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.098 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso mean: 30.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.9443 Å2-0 Å2-4.5536 Å2
2---3.8882 Å20 Å2
3---4.8326 Å2
Refinement stepCycle: LAST / Resolution: 1.85→36.734 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2079 0 81 260 2420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072237
X-RAY DIFFRACTIONf_angle_d1.0223015
X-RAY DIFFRACTIONf_dihedral_angle_d19.475863
X-RAY DIFFRACTIONf_chiral_restr0.072329
X-RAY DIFFRACTIONf_plane_restr0.004376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.91610.21221370.19872428X-RAY DIFFRACTION89
1.9161-1.99280.24741440.18382497X-RAY DIFFRACTION92
1.9928-2.08350.20271190.16342545X-RAY DIFFRACTION94
2.0835-2.19340.16871330.15182580X-RAY DIFFRACTION95
2.1934-2.33080.2091590.14582601X-RAY DIFFRACTION96
2.3308-2.51070.18831490.15852617X-RAY DIFFRACTION97
2.5107-2.76330.22421220.16612690X-RAY DIFFRACTION97
2.7633-3.16290.16821370.15692639X-RAY DIFFRACTION97
3.1629-3.98420.17211520.14092614X-RAY DIFFRACTION96
3.9842-36.74120.19841390.17352635X-RAY DIFFRACTION94
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)
12.22060.48261.44681.7983-0.63351.63660.0387-0.4716-0.3490.19120.0046-0.2664-0.0568-0.1947-0.0450.12850.0143-0.02860.26020.05920.193129.42141.7458-10.0301
21.6539-0.88180.18651.04940.27390.1905-0.0264-0.16060.03620.01520.0469-0.10610.00120.0411-0.01410.03970.00340.00190.08390.0060.060918.11578.6281-20.2626
30.7269-0.2553-0.02382.02730.02550.4598-0.0626-0.1647-0.00770.17430.05560.0028-0.03880.07180.00150.07880.01430.00670.0883-0.00860.03816.57821.1165-18.8555
45.4163-1.00610.1692.0460.11340.3230.0344-0.79030.94140.0402-0.1886-0.08410.20730.19960.08090.20360.01750.00330.2939-0.07060.299226.091510.5869-18.1903
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 3:63)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 64:157)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 158:279)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 1280)

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