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- PDB-3h9f: Crystal Structure of Human Dual Specificity Protein Kinase (TTK) ... -

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Basic information

Entry
Database: PDB / ID: 3h9f
TitleCrystal Structure of Human Dual Specificity Protein Kinase (TTK) in complex with a pyrimido-diazepin ligand
ComponentsDual specificity protein kinase TTK
KeywordsTRANSFERASE / TTK / hMPS1 / PYT / ESK / kinase / Dual Specificity / phosphotyrosine picked threonine kinase / SGC / Structural Genomics Consortium / ATP-binding / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase / Tyrosine-protein kinase
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 / kinetochore / spindle / protein tyrosine kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / ATP binding / identical protein binding / membrane / 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-92M / Dual specificity protein kinase TTK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsFilippakopoulos, P. / Soundararajan, M. / Keates, T. / Elkins, J.M. / King, O. / Fedorov, O. / Picaud, S.S. / Pike, A.C.W. / Yue, W. / Chaikuad, A. ...Filippakopoulos, P. / Soundararajan, M. / Keates, T. / Elkins, J.M. / King, O. / Fedorov, O. / Picaud, S.S. / Pike, A.C.W. / Yue, W. / Chaikuad, A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / Bountra, C. / Kwiatkowski, N. / Gray, N.S. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Nat.Chem.Biol. / Year: 2010
Title: Small-molecule kinase inhibitors provide insight into Mps1 cell cycle function.
Authors: Kwiatkowski, N. / Jelluma, N. / Filippakopoulos, P. / Soundararajan, M. / Manak, M.S. / Kwon, M. / Choi, H.G. / Sim, T. / Deveraux, Q.L. / Rottmann, S. / Pellman, D. / Shah, J.V. / Kops, G.J. ...Authors: Kwiatkowski, N. / Jelluma, N. / Filippakopoulos, P. / Soundararajan, M. / Manak, M.S. / Kwon, M. / Choi, H.G. / Sim, T. / Deveraux, Q.L. / Rottmann, S. / Pellman, D. / Shah, J.V. / Kops, G.J. / Knapp, S. / Gray, N.S.
History
DepositionApr 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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)36,8704
Polymers36,3551
Non-polymers5153
Water19811
1
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)147,48216
Polymers145,4214
Non-polymers2,06112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area5630 Å2
ΔGint-105 kcal/mol
Surface area48540 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.690, 110.750, 115.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1-

MG

DetailsMonomer

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Components

#1: Protein Dual specificity protein kinase TTK / Phosphotyrosine picked threonine-protein kinase / PYT


Mass: 36355.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MPS1L1, TTK / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: P33981, dual-specificity kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-92M / 9-cyclopentyl-2-(4-(4-hydroxypiperidin-1-yl)-2-methoxyphenylamino)-5-methyl-8,9-dihydro-5H-pyrimido[4,5-b][1,4]diazepin -6(7H)-one / 9-cyclopentyl-2-{[4-(4-hydroxypiperidin-1-yl)-2-methoxyphenyl]amino}-5-methyl-5,7,8,9-tetrahydro-6H-pyrimido[4,5-b][1,4 ]diazepin-6-one


Mass: 466.576 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H34N6O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.1 Å3/Da / Density % sol: 60.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 25% PEG3350, 0.2M MgCl2, 0.1M BT pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9782 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9782 Å / Relative weight: 1
ReflectionResolution: 2.6→41.414 Å / Num. all: 14244 / Num. obs: 14201 / % possible obs: 99.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 80.9 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 14.4
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 4 % / Rmerge(I) obs: 0.733 / Mean I/σ(I) obs: 2 / Num. unique all: 2042 / Rsym value: 0.417 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 40.87 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.6 Å41.41 Å
Translation2.6 Å41.41 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CEK

3cek


Resolution: 2.6→41 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.261 / WRfactor Rwork: 0.211 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.827 / SU B: 19.596 / SU ML: 0.199 / SU R Cruickshank DPI: 0.36 / SU Rfree: 0.266 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.36 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.253 709 5 %RANDOM
Rwork0.207 ---
all0.21 14267 --
obs0.21 14199 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 113.18 Å2 / Biso mean: 35.521 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--2.51 Å20 Å20 Å2
2--2.32 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.6→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2084 0 36 11 2131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222171
X-RAY DIFFRACTIONr_bond_other_d0.0010.021438
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.992950
X-RAY DIFFRACTIONr_angle_other_deg1.3593.0023505
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6815260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.3125.43592
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.58915.04373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.664155
X-RAY DIFFRACTIONr_chiral_restr0.0790.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212352
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02389
X-RAY DIFFRACTIONr_mcbond_it3.75231314
X-RAY DIFFRACTIONr_mcbond_other0.9193523
X-RAY DIFFRACTIONr_mcangle_it6.10452125
X-RAY DIFFRACTIONr_scbond_it10.1418857
X-RAY DIFFRACTIONr_scangle_it12.8411825
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.468 49 -
Rwork0.456 964 -
all-1013 -
obs--99.8 %
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)
18.6782-1.4429-2.0673.7446-3.05037.6079-0.1436-0.74180.24270.26930.2649-0.6707-0.11540.8005-0.12130.1908-0.0469-0.08370.3456-0.09310.31211.630724.49546.7227
26.83940.38113.15671.46970.04494.45240.0355-0.29910.2162-0.0288-0.02240.1825-0.1668-0.215-0.01310.15560.05020.03180.06180.03730.0762-3.757423.163838.8088
34.7058-1.46861.38594.0866-0.62524.75790.18990.2403-0.8595-0.0747-0.01810.10920.65690.0573-0.17180.2093-0.0428-0.01590.16260.03060.2864-12.14419.243130.2134
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A515 - 569
2X-RAY DIFFRACTION2A570 - 663
3X-RAY DIFFRACTION3A664 - 794

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