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- PDB-2x9e: HUMAN MPS1 IN COMPLEX WITH NMS-P715 -

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Basic information

Entry
Database: PDB / ID: 2x9e
TitleHUMAN MPS1 IN COMPLEX WITH NMS-P715
ComponentsDUAL SPECIFICITY PROTEIN KINASE TTK
KeywordsTRANSFERASE / KINASE / SERINE/THREONINE-PROTEIN KINASE / TYROSINE-PROTEIN KINASE / MITOTIC CHECKPOINT
Function / homology
Function and homology information


protein localization to meiotic spindle midzone / meiotic spindle assembly checkpoint signaling / kinetochore binding / female meiosis chromosome segregation / protein localization to kinetochore / dual-specificity kinase / spindle organization / mitotic spindle assembly checkpoint signaling / protein serine/threonine/tyrosine kinase activity / mitotic spindle organization ...protein localization to meiotic spindle midzone / meiotic spindle assembly checkpoint signaling / kinetochore binding / female meiosis chromosome segregation / protein localization to kinetochore / dual-specificity kinase / spindle organization / mitotic spindle assembly checkpoint signaling / protein serine/threonine/tyrosine kinase activity / mitotic spindle organization / chromosome segregation / spindle / kinetochore / protein tyrosine kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / ATP binding / membrane / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Protein kinase Mps1 family / Tetratricopeptide-like helical domain superfamily / 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 Mps1 family / Tetratricopeptide-like helical domain superfamily / 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, ATP binding site / Protein kinases ATP-binding region signature. / 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-SVE / Dual specificity protein kinase TTK
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsColombo, R. / Caldarelli, M. / Mennecozzi, M. / Giorgini, M.L. / Sola, F. / Cappella, P. / Perrera, C. / DePaolini, S.R. / Rusconi, L. / Cucchi, U. ...Colombo, R. / Caldarelli, M. / Mennecozzi, M. / Giorgini, M.L. / Sola, F. / Cappella, P. / Perrera, C. / DePaolini, S.R. / Rusconi, L. / Cucchi, U. / Avanzi, N. / Bertrand, J.A. / Bossi, R.T. / Pesenti, E. / Galvani, A. / Isacchi, A. / Colotta, F. / Donati, D. / Moll, J.
CitationJournal: Cancer Res. / Year: 2010
Title: Targeting the Mitotic Checkpoint for Cancer Therapy with Nms-P715, an Inhibitor of Mps1 Kinase.
Authors: Colombo, R. / Caldarelli, M. / Mennecozzi, M. / Giorgini, M.L. / Sola, F. / Cappella, P. / Perrera, C. / Depaolini, S.R. / Rusconi, L. / Cucchi, U. / Avanzi, N. / Bertrand, J.A. / Bossi, R.T. ...Authors: Colombo, R. / Caldarelli, M. / Mennecozzi, M. / Giorgini, M.L. / Sola, F. / Cappella, P. / Perrera, C. / Depaolini, S.R. / Rusconi, L. / Cucchi, U. / Avanzi, N. / Bertrand, J.A. / Bossi, R.T. / Pesenti, E. / Galvani, A. / Isacchi, A. / Colotta, F. / Donati, D. / Moll, J.
History
DepositionMar 17, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 27, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 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: DUAL SPECIFICITY PROTEIN KINASE TTK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9162
Polymers36,2401
Non-polymers6771
Water362
1
A: DUAL SPECIFICITY PROTEIN KINASE TTK
hetero molecules

A: DUAL SPECIFICITY PROTEIN KINASE TTK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8334
Polymers72,4792
Non-polymers1,3532
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3320 Å2
ΔGint-16 kcal/mol
Surface area24930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.665, 113.362, 72.485
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein DUAL SPECIFICITY PROTEIN KINASE TTK / MPS1 / PHOSPHOTYROSINE PICKED THREONINE-PROTEIN KINASE / PYT


Mass: 36239.652 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN 514-828
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PVLGSTG / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P33981, dual-specificity kinase
#2: Chemical ChemComp-SVE / N-(2,6-DIETHYLPHENYL)-1-METHYL-8-({4-[(1-METHYLPIPERIDIN-4-YL)CARBAMOYL]-2-(TRIFLUOROMETHOXY)PHENYL}AMINO)-4,5-DIHYDRO-1H-PYRAZOLO[4,3-H]QUINAZOLINE-3-CARBOXAMIDE


Mass: 676.731 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H39F3N8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3 Å3/Da / Density % sol: 59 % / Description: NONE
Crystal growpH: 6.5 / Details: 12% PEG 20000, 0.1 M MES PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 3.1→40 Å / Num. obs: 7419 / % possible obs: 90.4 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 81.2 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.1
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.89 / % possible all: 56.4

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Processing

Software
NameVersionClassification
CNS2005refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CEK

3cek


Resolution: 3.1→19.99 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 1573647.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.306 388 5.2 %RANDOM
Rwork0.215 ---
obs0.215 7416 90.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.0765 Å2 / ksol: 0.264847 e/Å3
Displacement parametersBiso mean: 73.9 Å2
Baniso -1Baniso -2Baniso -3
1--16.79 Å20 Å20 Å2
2--32.58 Å20 Å2
3----15.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.6 Å
Refinement stepCycle: LAST / Resolution: 3.1→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2068 0 49 2 2119
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.481.5
X-RAY DIFFRACTIONc_mcangle_it2.672
X-RAY DIFFRACTIONc_scbond_it1.942
X-RAY DIFFRACTIONc_scangle_it3.292.5
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.047 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.333 51 5.9 %
Rwork0.349 818 -
obs--65 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3715.PAR715.TOP

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