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- PDB-5ap2: Naturally Occurring Mutations in the MPS1 Gene Predispose Cells t... -

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Basic information

Entry
Database: PDB / ID: 5ap2
TitleNaturally Occurring Mutations in the MPS1 Gene Predispose Cells to Kinase Inhibitor Drug Resistance.
ComponentsDUAL SPECIFICITY PROTEIN KINASE TTK
KeywordsTRANSFERASE / MPS1 / PROTEIN KINASE / MITOSIS / DRUG RESISTANCE
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-PWU / Dual specificity protein kinase TTK
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGurden, M.D. / Westwood, I.M. / Faisal, A. / Naud, S. / Cheung, K.J. / McAndrew, C. / Wood, A. / Schmitt, J. / Boxall, K. / Mak, G. ...Gurden, M.D. / Westwood, I.M. / Faisal, A. / Naud, S. / Cheung, K.J. / McAndrew, C. / Wood, A. / Schmitt, J. / Boxall, K. / Mak, G. / Workman, P. / Burke, R. / Hoelder, S. / Blagg, J. / van Montfort, R.L.M. / Linardopoulos, S.
CitationJournal: Cancer Res. / Year: 2015
Title: Naturally Occurring Mutations in the Mps1 Gene Predispose Cells to Kinase Inhibitor Drug Resistance.
Authors: Gurden, M.D. / Westwood, I.M. / Faisal, A. / Naud, S. / Cheung, K.J. / Mcandrew, C. / Wood, A. / Schmitt, J. / Boxall, K. / Mak, G. / Workman, P. / Burke, R. / Hoelder, S. / Blagg, J. / Van ...Authors: Gurden, M.D. / Westwood, I.M. / Faisal, A. / Naud, S. / Cheung, K.J. / Mcandrew, C. / Wood, A. / Schmitt, J. / Boxall, K. / Mak, G. / Workman, P. / Burke, R. / Hoelder, S. / Blagg, J. / Van Montfort, R.L.M. / Linardopoulos, S.
History
DepositionSep 14, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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)36,5852
Polymers36,1151
Non-polymers4701
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.060, 103.960, 111.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 36115.258 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, UNP RESIDUES 519-808
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): AI / References: UniProt: P33981, dual-specificity kinase
#2: Chemical ChemComp-PWU / ISOPROPYL 6-((4-(1,2-DIMETHYL-1H-IMIDAZOL-5-YL)PHENYL)AMINO)-2-(1-METHYL-1H-PYRAZOL-4-YL)-1H-PYRROLO[3,2-C]PYRIDINE-1-CARBOXYLATE


Mass: 469.538 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H27N7O2
Sequence detailsTHE SEQUENCE INCLUDING HEXAHISTIDINE TAG IS AS DESCRIBED IN NAT. CHEM. BIOL. 2010, 6, 259-368.

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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: 2.82 Å3/Da / Density % sol: 56.31 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1M BIS-TRIS PROPANE PH 7.5, 22% (W/V) PEG3350, 0.1M MGCL2, 0.1M NA FORMATE CO-CRYSTAL WITH 1MM INHIBITOR

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.8→39.1 Å / Num. obs: 10320 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 125.45 Å2 / Rmerge(I) obs: 0.24 / Net I/σ(I): 3
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 0.7 / % possible all: 99.3

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C4J

4c4j


Resolution: 2.8→39.1 Å / Cor.coef. Fo:Fc: 0.9468 / Cor.coef. Fo:Fc free: 0.9063 / SU R Cruickshank DPI: 0.478 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.466 / SU Rfree Blow DPI: 0.302 / SU Rfree Cruickshank DPI: 0.308
RfactorNum. reflection% reflectionSelection details
Rfree0.2539 497 4.82 %RANDOM
Rwork0.1945 ---
obs0.1973 10317 99.68 %-
Displacement parametersBiso mean: 120.73 Å2
Baniso -1Baniso -2Baniso -3
1--2.4872 Å20 Å20 Å2
2--1.6747 Å20 Å2
3---0.8125 Å2
Refine analyzeLuzzati coordinate error obs: 0.584 Å
Refinement stepCycle: LAST / Resolution: 2.8→39.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1915 0 35 0 1950
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011999HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.142735HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d630SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes46HARMONIC2
X-RAY DIFFRACTIONt_gen_planes331HARMONIC5
X-RAY DIFFRACTIONt_it1999HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.59
X-RAY DIFFRACTIONt_other_torsion21.03
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion274SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2200SEMIHARMONIC4
LS refinement shellResolution: 2.8→3.13 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2686 152 5.32 %
Rwork0.2223 2707 -
all0.2247 2859 -
obs--99.68 %
Refinement TLS params.

T23: 0.152 Å2 / 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)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.24671.10851.19865.4244-2.91046.2625-0.0604-0.4715-0.3080.5442-0.1428-0.44850.0514-0.00670.2032-0.3037-0.0521-0.00580.1452-0.279810.2741-30.3881-13.255
28.30771.43722.36442.8494-2.17483.9976-0.0594-0.38920.24610.15210.29040.2577-0.2102-0.5441-0.2311-0.2937-0.0150.05870.1332-0.304-4.1216-31.6452-18.3652
32.4797-0.83440.32413.9738-2.56653.65970.08860.2788-0.4317-0.5320.2190.4670.5380.0556-0.3077-0.285-0.0277-0.03550.0569-0.1996-12.6662-43.4889-29.2852
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|516 - 579}
2X-RAY DIFFRACTION2{A|580 - 662}
3X-RAY DIFFRACTION3{A|663 - 794}

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