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- PDB-2w5a: Human Nek2 kinase ADP-bound -

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Basic information

Entry
Database: PDB / ID: 2w5a
TitleHuman Nek2 kinase ADP-bound
ComponentsSERINE/THREONINE-PROTEIN KINASE NEK2
KeywordsTRANSFERASE / SER/THR PROTEIN KINASE / KINASE / NUCLEUS / MEIOSIS / MITOSIS / CYTOPLASM / SERINE/THREONINE-PROTEIN KINASE / METAL-BINDING / PHOSPHOPROTEIN / NUCLEOTIDE-BINDING / MAGNESIUM / CELL CYCLE / ATP-BINDING / CENTROSOME SPLITTING / ALTERNATIVE SPLICING / COILED COIL / POLYMORPHISM / 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 / 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 / : / Recruitment of NuMA to mitotic centrosomes / positive regulation of telomere maintenance via telomerase / Anchoring of the basal body to the plasma membrane / 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 / nucleus / metal ion binding / cytoplasm / cytosol
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
ADENOSINE-5'-DIPHOSPHATE / Serine/threonine-protein kinase Nek2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.55 Å
AuthorsWestwood, I. / Bayliss, 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 1.1Jul 7, 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 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,3627
Polymers32,6621
Non-polymers7006
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.467, 57.103, 80.213
Angle α, β, γ (deg.)90.00, 132.99, 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: 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) / Plasmid: PET30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P51955, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsC-TERMINAL LEHHHHHH AFFINITY TAG FROM VECTOR SEQUENCE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 57.04 % / 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: ID14-2 / Wavelength: 0.92
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.55→26.23 Å / Num. obs: 45663 / % possible obs: 95.6 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Biso Wilson estimate: 14.14 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.8

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: OTHER / Resolution: 1.55→24.74 Å / SU ML: 0.18 / σ(F): 0.02 / Phase error: 19.18 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.19 2241 5.1 %
Rwork0.172 --
obs0.173 43905 91.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.36 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 25.23 Å2
Baniso -1Baniso -2Baniso -3
1--1.7541 Å2-0 Å2-3.968 Å2
2---2.5531 Å20 Å2
3---4.3073 Å2
Refinement stepCycle: LAST / Resolution: 1.55→24.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2175 0 44 355 2574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042396
X-RAY DIFFRACTIONf_angle_d0.9773245
X-RAY DIFFRACTIONf_dihedral_angle_d17.264916
X-RAY DIFFRACTIONf_chiral_restr0.066351
X-RAY DIFFRACTIONf_plane_restr0.004413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.58370.2295840.22171632X-RAY DIFFRACTION59
1.5837-1.62050.2445900.21631935X-RAY DIFFRACTION68
1.6205-1.66110.24871170.20162222X-RAY DIFFRACTION79
1.6611-1.7060.211270.18992592X-RAY DIFFRACTION91
1.706-1.75610.24331530.18262617X-RAY DIFFRACTION94
1.7561-1.81280.20291530.17582668X-RAY DIFFRACTION95
1.8128-1.87760.18211210.17092728X-RAY DIFFRACTION96
1.8776-1.95270.19871410.17322726X-RAY DIFFRACTION97
1.9527-2.04160.20041590.15852794X-RAY DIFFRACTION98
2.0416-2.14910.17781480.15752771X-RAY DIFFRACTION99
2.1491-2.28370.17161640.15562808X-RAY DIFFRACTION99
2.2837-2.45990.19121610.16052791X-RAY DIFFRACTION99
2.4599-2.70720.16471370.17012829X-RAY DIFFRACTION99
2.7072-3.09820.1971850.16692806X-RAY DIFFRACTION99
3.0982-3.9010.1711570.15852838X-RAY DIFFRACTION100
3.901-24.74250.17521440.16862907X-RAY DIFFRACTION99
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)
11.6560.60710.02470.61980.06540.2259-0.14560.2028-0.2518-0.0670.1025-0.0319-0.0195-0.09950.03560.0422-0.030.0320.0685-0.03770.0673-32.72130.363516.2181
2-0.0260.0484-0.32320.9910.09160.2414-0.25560.0070.1698-0.14420.1689-0.18850.0345-0.02280.00850.1689-0.0152-0.05750.2915-0.03040.0843-22.79733.30281.106
31.10180.63650.10680.84530.43391.2668-0.0090.07210.0237-0.0086-0.03240.08020.0131-0.16960.09220.0189-0.00810.01090.0354-0.00590.0251-19.03598.233719.8479
40.8649-0.34050.17672.74480.1495-1.42550.04580.18340.0222-0.46540.0028-0.06190.0453-0.04040.01840.0902-0.01330.02110.08470.01010.0096-14.62569.004818.3151
50.3074-0.05290.16950.6846-0.0225-0.1826-0.16920.1730.0769-0.4240.26730.29990.0197-0.0954-0.01450.2105-0.0819-0.07550.20390.03640.1201-18.623119.43867.5994
62.7771-0.4011-0.07333.22750.544-0.96380.00480.37560.006-0.51450.03210.1654-0.1405-0.0981-0.05860.1103-0.02-0.01880.05420.00740.0115-7.13421.635914.9434
70.90110.38510.0682-0.08120.47071.0777-0.07150.11380.06580.00550.0012-0.0488-0.185-0.0345-0.01010.0629-0.00720.00530.02680.00790.0161-5.98328.632521.6295
80.41210.48-0.05060.9248-0.5070.5395-0.05620.0613-0.1114-0.08090.0665-0.20170.08880.00630.03640.0472-0.01320.03350.0221-0.01160.0471-0.60112.089123.3782
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 3-36
2X-RAY DIFFRACTION2CHAIN A AND RESID 37-63
3X-RAY DIFFRACTION3CHAIN A AND RESID 64-128
4X-RAY DIFFRACTION4CHAIN A AND RESID 129-156
5X-RAY DIFFRACTION5CHAIN A AND RESID 157-184
6X-RAY DIFFRACTION6CHAIN A AND RESID 185-214
7X-RAY DIFFRACTION7CHAIN A AND RESID 215-252
8X-RAY DIFFRACTION8CHAIN A AND RESID 253-279

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