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- PDB-2w5b: Human Nek2 kinase ATPgammaS-bound -

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Basic information

Entry
Database: PDB / ID: 2w5b
TitleHuman Nek2 kinase ATPgammaS-bound
ComponentsSERINE/THREONINE-PROTEIN KINASE NEK2
KeywordsTRANSFERASE / MEIOSIS / MITOSIS / CYTOPLASM / METAL-BINDING / PHOSPHOPROTEIN / NUCLEOTIDE-BINDING / MAGNESIUM / CELL CYCLE / ATP-BINDING / CENTROSOME SPLITTING / CELL DIVISION
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 / microtubule / protein autophosphorylation / 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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Serine/threonine-protein kinase Nek2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.4 Å
AuthorsBayliss, R.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Insights Into the Conformational Variability and Regulation of Human Nek2 Kinase.
Authors: Westwood, I. / Cheary, D.M. / Baxter, J.E. / Richards, M.W. / Van Montfort, R.L. / Fry, A.M. / Bayliss, R.
History
DepositionDec 8, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Version format compliance
Revision 1.2May 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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)33,2154
Polymers32,6321
Non-polymers5833
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)99.602, 57.064, 80.802
Angle α, β, γ (deg.)90.00, 133.45, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein SERINE/THREONINE-PROTEIN KINASE NEK2 / NIMA-RELATED PROTEIN KINASE 2 / NIMA-LIKE PROTEIN KINASE 1 / HSPK 21 / NEK2


Mass: 32632.451 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 1-271 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P51955, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 175 TO ALA
Sequence detailsC-TERMINAL LEHHHHHH AFFINITY TAG FROM VECTOR SEQUENCE T175A MUTATION

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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: 2.56 Å3/Da / Density % sol: 51.91 % / Description: NONE
Crystal growDetails: 50 MM TRIS, PH 8.5 2-10% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.4→49 Å / Num. obs: 12943 / % possible obs: 99.2 % / Observed criterion σ(I): 3 / Redundancy: 2.5 % / Biso Wilson estimate: 15.71 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 3.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.4→49.56 Å / SU ML: 0.36 / σ(F): 0.13 / Phase error: 21.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.245 612 4.9 %
Rwork0.183 --
obs0.186 12490 95.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.56 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 27.52 Å2
Baniso -1Baniso -2Baniso -3
1--5.4142 Å2-0 Å2-3.0308 Å2
2---7.8106 Å2-0 Å2
3----3.9652 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2193 0 33 166 2392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062287
X-RAY DIFFRACTIONf_angle_d0.9913095
X-RAY DIFFRACTIONf_dihedral_angle_d20.276849
X-RAY DIFFRACTIONf_chiral_restr0.063334
X-RAY DIFFRACTIONf_plane_restr0.004393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.64150.26931690.18662896X-RAY DIFFRACTION95
2.6415-3.02370.25521400.19652980X-RAY DIFFRACTION96
3.0237-3.80940.24591550.17672974X-RAY DIFFRACTION96
3.8094-49.57280.22241480.16733028X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 15.9491 Å / Origin y: 14.1695 Å / Origin z: -16.2354 Å
111213212223313233
T0.0838 Å2-0.005 Å20.0212 Å2-0.1041 Å20.0034 Å2--0.0652 Å2
L1.0353 °2-0.62 °20.1774 °2-0.967 °2-0.1517 °2--0.2023 °2
S-0.0582 Å °-0.1292 Å °-0.0649 Å °0.1357 Å °0.0679 Å °0.0099 Å °-0.0575 Å °0.0589 Å °-0.0128 Å °
Refinement TLS groupSelection details: CHAIN A

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