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- PDB-2xnp: Structure of Nek2 bound to CCT244858 -

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Basic information

Entry
Database: PDB / ID: 2xnp
TitleStructure of Nek2 bound to CCT244858
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 ...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 / 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 / condensed nuclear chromosome / meiotic cell cycle / chromosome segregation / kinetochore / spindle pole / Regulation of PLK1 Activity at G2/M Transition / mitotic cell cycle / midbody / protein phosphatase binding / protein autophosphorylation / microtubule / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation / cell division / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / nucleolus / protein-containing complex / nucleoplasm / ATP binding / nucleus / metal ion binding / 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. ...: / 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-WCX / Serine/threonine-protein kinase Nek2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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)33,65311
Polymers32,6621
Non-polymers99110
Water4,035224
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.640, 56.880, 81.840
Angle α, β, γ (deg.)90.00, 133.63, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2080-

HOH

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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-WCX / 4-{5-[(1-METHYLPIPERIDIN-4-YL)OXY]-1H-BENZIMIDAZOL-1-YL}-2-{(1R)-1-[2-(TRIFLUOROMETHYL)PHENYL]ETHOXY}BENZAMIDE


Mass: 538.561 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H29F3N4O3
#3: Chemical
ChemComp-CL / CHLORIDE ION


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


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


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.08 % / 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: Apr 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.9→46.52 Å / Num. obs: 26646 / % possible obs: 99.4 % / Observed criterion σ(I): 6 / Redundancy: 3.6 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.5 / % possible all: 99.7

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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: 1.98→36.784 Å / SU ML: 0.21 / σ(F): 0.03 / Phase error: 18.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2012 1165 5.1 %
Rwork0.1566 --
obs0.1589 22973 96.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.124 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso mean: 30.82 Å2
Baniso -1Baniso -2Baniso -3
1--1.0725 Å2-0 Å2-6.3588 Å2
2---4.891 Å20 Å2
3---5.9635 Å2
Refinement stepCycle: LAST / Resolution: 1.98→36.784 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2075 0 63 224 2362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012203
X-RAY DIFFRACTIONf_angle_d1.2122966
X-RAY DIFFRACTIONf_dihedral_angle_d19.784860
X-RAY DIFFRACTIONf_chiral_restr0.087317
X-RAY DIFFRACTIONf_plane_restr0.005371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.07010.211570.1692625X-RAY DIFFRACTION94
2.0701-2.17920.22561430.16212638X-RAY DIFFRACTION95
2.1792-2.31580.20521340.14832690X-RAY DIFFRACTION96
2.3158-2.49450.17661170.14492745X-RAY DIFFRACTION97
2.4945-2.74550.20851450.14622750X-RAY DIFFRACTION97
2.7455-3.14260.21931490.14882769X-RAY DIFFRACTION99
3.1426-3.95860.18161380.14492789X-RAY DIFFRACTION99
3.9586-36.79040.19081820.1672802X-RAY DIFFRACTION98
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)
11.8964-0.40791.35991.07190.2561.61450.05890.6825-0.4494-0.16580.03790.38490.050.1922-0.05230.1079-0.0168-0.05510.2812-0.09290.1845-29.4606-10.854210.1849
21.69841.00320.15421.13040.01120.0328-0.01130.19890.1334-0.03640.02090.13360.043-0.06560.00210.042-0.00530.00230.0880.00010.0378-18.1899-3.568520.2085
30.98340.5889-0.22281.2230.25810.5304-0.08680.17130.015-0.07260.0519-0.026-0.0771-0.07080.03080.0547-0.00740.00680.0560.00390.0269-6.06029.052419.3764
41.8860.5218-2.16420.8693-0.22445.1072-0.27070.38760.31130.03620.08190.0659-0.043-0.42410.15460.1081-0.0013-0.00860.16570.0510.1712-26.4379-2.404618.7578
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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