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- PDB-2jav: Human Kinase with pyrrole-indolinone ligand -

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Basic information

Entry
Database: PDB / ID: 2jav
TitleHuman Kinase with pyrrole-indolinone ligand
ComponentsSERINE/THREONINE-PROTEIN KINASE NEK2
KeywordsTRANSFERASE / PHOSPHORYLATION / NUCLEOTIDE-BINDING / ATP-BINDING / CELL DIVISION / METAL-BINDING / NUCLEAR PROTEIN / SERINE/THREONINE-PROTEIN KINASE / SERINE/THREONINE PROTEIN KINASE / KINASE / MEIOSIS / MITOSIS / MAGNESIUM / 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-5Z5 / Serine/threonine-protein kinase Nek2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPike, A.C.W. / Rellos, P. / Das, S. / Fedorov, O. / Papagrigoriou, E. / Debreczeni, J.E. / Turnbull, A.P. / Gorrec, F. / Bray, J. / Sundstrom, M. ...Pike, A.C.W. / Rellos, P. / Das, S. / Fedorov, O. / Papagrigoriou, E. / Debreczeni, J.E. / Turnbull, A.P. / Gorrec, F. / Bray, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / von Delft, F. / Knapp, S.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structure and Regulation of the Human Nek2 Centrosomal Kinase
Authors: Rellos, P. / Ivins, F.J. / Baxter, J.E. / Pike, A.C.W. / Nott, T.J. / Parkinson, D.-M. / Das, S. / Howell, S. / Fedorov, O. / Shen, Q.Y. / Fry, A.M. / Knapp, S. / Smerdon, S.J.
History
DepositionNov 30, 2006Deposition site: PDBE / Processing site: PDBE
SupersessionDec 4, 2006ID: 2CL1
Revision 1.0Dec 4, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)32,9622
Polymers32,6321
Non-polymers3301
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)41.634, 56.924, 66.012
Angle α, β, γ (deg.)90.00, 95.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


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
#2: Chemical ChemComp-5Z5 / 5-[(Z)-(5-CHLORO-2-OXO-1,2-DIHYDRO-3H-INDOL-3-YLIDENE)METHYL]-N-(DIETHYLAMINO)ETHYL]-2,4-DIMETHYL-1H-PYRROLE-3-CARBOXAMIDE


Mass: 329.781 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16ClN3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 175 TO ALA
Sequence detailsC-TERMINAL HEXA-HISTIDINE TAG

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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: 2.39 Å3/Da / Density % sol: 48.52 %
Crystal growMethod: vapor diffusion, sitting drop
Details: 10% PEG6000, 200 MM MGCL2. SITTING DROPS, 150NL AND 50NL PROTEIN AND RESERVOIR MIX.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.95
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 24, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.2→65 Å / Num. obs: 15620 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 32.55 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.4 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OL7

1ol7


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.883 / SU B: 11.818 / SU ML: 0.164 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.DIETHYLAMINO TAIL OF LIGAND IS DISORDERED AND HAS NOT BEEN INCLUDED IN THE FINAL MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.277 796 5.1 %RANDOM
Rwork0.214 ---
obs0.217 14883 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20 Å2-1.77 Å2
2---1.95 Å20 Å2
3---0.65 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2014 0 23 107 2144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212119
X-RAY DIFFRACTIONr_bond_other_d1.2251.982858
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5145249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.67323.204103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.23215380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.31518
X-RAY DIFFRACTIONr_chiral_restr0.0780.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021604
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1870.2932
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.21423
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2117
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5521.51297
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.89522019
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.2383970
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9224.5839
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.263 62
Rwork0.237 1019
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)
113.4988-3.14664.85134.4903-1.43484.67561.03861.6194-1.5073-1.4248-0.47280.67320.73130.2933-0.56580.44290.0085-0.3760.0551-0.18950.1932-3.95912.285910.5005
22.54860.05260.03784.35580.2132.0580.04450.35360.0935-0.5251-0.01890.0503-0.0078-0.0305-0.0256-0.15750.00320.0174-0.14170.0179-0.208212.81619.160822.8707
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 90
2X-RAY DIFFRACTION2A91 - 279

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