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- PDB-4jt3: Crystal Structure of TTK kinase domain with an inhibitor: 400740 -

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Basic information

Entry
Database: PDB / ID: 4jt3
TitleCrystal Structure of TTK kinase domain with an inhibitor: 400740
ComponentsDual specificity protein kinase TTK
KeywordsTransferase/Transferase Inhibitor / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


protein localization to meiotic spindle midzone / meiotic spindle assembly checkpoint signaling / repair of mitotic kinetochore microtubule attachment defect / kinetochore binding / female meiosis chromosome segregation / protein localization to kinetochore / dual-specificity kinase / spindle organization / mitotic spindle assembly checkpoint signaling / positive regulation of SMAD protein signal transduction ...protein localization to meiotic spindle midzone / meiotic spindle assembly checkpoint signaling / repair of mitotic kinetochore microtubule attachment defect / kinetochore binding / female meiosis chromosome segregation / protein localization to kinetochore / dual-specificity kinase / spindle organization / mitotic spindle assembly checkpoint signaling / positive regulation of SMAD protein signal transduction / protein serine/threonine/tyrosine kinase activity / mitotic spindle organization / chromosome segregation / kinetochore / spindle / protein tyrosine kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / ATP binding / identical protein binding / nucleus / membrane / cytoplasm
Similarity search - Function
Protein kinase Mps1 family / Tetratricopeptide-like helical domain superfamily / 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 Mps1 family / Tetratricopeptide-like helical domain superfamily / 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, 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-1PH / PHOSPHATE ION / Dual specificity protein kinase TTK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsQiu, W. / Harris-Brandts, M. / Feher, M. / Awrey, D.E. / Chirgadze, N.Y.
CitationJournal: To be Published
Title: Crystal Structure of TTK kinase domain with an inhibitor: 400740
Authors: Qiu, W. / Harris-Brandts, M. / Feher, M. / Awrey, D.E. / Chirgadze, N.Y.
History
DepositionMar 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)33,86616
Polymers32,4591
Non-polymers1,40715
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Dual specificity protein kinase TTK
hetero molecules

A: Dual specificity protein kinase TTK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,73332
Polymers64,9192
Non-polymers2,81430
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area7370 Å2
ΔGint-30 kcal/mol
Surface area24910 Å2
MethodPISA
3
A: Dual specificity protein kinase TTK
hetero molecules

A: Dual specificity protein kinase TTK
hetero molecules

A: Dual specificity protein kinase TTK
hetero molecules

A: Dual specificity protein kinase TTK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,46564
Polymers129,8374
Non-polymers5,62860
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area17790 Å2
ΔGint-52 kcal/mol
Surface area46760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.750, 105.931, 113.018
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


Mass: 32459.303 Da / Num. of mol.: 1 / Fragment: kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTK, MPS1, MPS1L1 / Production host: Escherichia coli (E. coli) / References: UniProt: P33981, dual-specificity kinase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-1PH / 2-phenyl-N-[3-(3-sulfamoylphenyl)-2H-indazol-5-yl]acetamide


Mass: 406.458 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H18N4O3S
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3.26 Å3/Da / Density % sol: 62.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.53
Details: 0.2M NaCl 0.1M Na/K phosphate pH 5.53 6% PEG5000 MME 2.5% Glycerol 3% ethylene glycol, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9794 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jan 30, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 21959 / Num. obs: 21849 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 50.85 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 18.3
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 2 / Num. unique all: 2723 / % possible all: 99.2

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Processing

Software
NameVersionClassification
MxDCdata collection
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→23.78 Å / Cor.coef. Fo:Fc: 0.9083 / Cor.coef. Fo:Fc free: 0.9045 / SU R Cruickshank DPI: 0.214 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2514 1121 5.13 %RANDOM
Rwork0.2381 ---
all0.2388 21961 --
obs0.2388 21834 99.55 %-
Displacement parametersBiso mean: 68.98 Å2
Baniso -1Baniso -2Baniso -3
1-13.7729 Å20 Å20 Å2
2---27.9529 Å20 Å2
3---14.18 Å2
Refine analyzeLuzzati coordinate error obs: 0.395 Å
Refinement stepCycle: LAST / Resolution: 2.2→23.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2076 0 89 30 2195
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082199HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.912954HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1029SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes61HARMONIC2
X-RAY DIFFRACTIONt_gen_planes293HARMONIC5
X-RAY DIFFRACTIONt_it2199HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2
X-RAY DIFFRACTIONt_other_torsion3.41
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion279SEMIHARMONIC5
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_contact2397SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.31 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2964 162 5.65 %
Rwork0.2828 2703 -
all0.2835 2865 -
obs--99.55 %

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