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- PDB-3vqu: CRYSTAL STRUCTURE OF HUMAN MPS1 CATALYTIC DOMAIN IN COMPLEX WITH ... -

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Basic information

Entry
Database: PDB / ID: 3vqu
TitleCRYSTAL STRUCTURE OF HUMAN MPS1 CATALYTIC DOMAIN IN COMPLEX WITH 4-[(4-amino-5-cyano-6-ethoxypyridin-2- yl)amino]benzamide
ComponentsDual specificity protein kinase TTK
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / KINASE / SERINE/THREONINE-PROTEIN KINASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 / 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
IODIDE ION / Chem-O22 / Dual specificity protein kinase TTK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsKusakabe, K. / Ide, N. / Daigo, Y. / Itoh, T. / Higashino, K. / Okano, Y. / Tadano, G. / Tachibana, Y. / Sato, Y. / Inoue, M. ...Kusakabe, K. / Ide, N. / Daigo, Y. / Itoh, T. / Higashino, K. / Okano, Y. / Tadano, G. / Tachibana, Y. / Sato, Y. / Inoue, M. / Wada, T. / Iguchi, M. / Kanazawa, T. / Ishioka, Y. / Dohi, K. / Tagashira, S. / Kido, Y. / Sakamoto, S. / Yasuo, K. / Maeda, M. / Yamamoto, T. / Higaki, M. / Endoh, T. / Ueda, K. / Shiota, T. / Murai, H. / Nakamura, Y.
CitationJournal: Acs Med.Chem.Lett. / Year: 2012
Title: Diaminopyridine-based potent and selective mps1 kinase inhibitors binding to an unusual flipped-Peptide conformation.
Authors: Kusakabe, K. / Ide, N. / Daigo, Y. / Itoh, T. / Higashino, K. / Okano, Y. / Tadano, G. / Tachibana, Y. / Sato, Y. / Inoue, M. / Wada, T. / Iguchi, M. / Kanazawa, T. / Ishioka, Y. / Dohi, K. ...Authors: Kusakabe, K. / Ide, N. / Daigo, Y. / Itoh, T. / Higashino, K. / Okano, Y. / Tadano, G. / Tachibana, Y. / Sato, Y. / Inoue, M. / Wada, T. / Iguchi, M. / Kanazawa, T. / Ishioka, Y. / Dohi, K. / Tagashira, S. / Kido, Y. / Sakamoto, S. / Yasuo, K. / Maeda, M. / Yamamoto, T. / Higaki, M. / Endoh, T. / Ueda, K. / Shiota, T. / Murai, H. / Nakamura, Y.
History
DepositionMar 30, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.2Mar 20, 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

Downloads & links

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Assembly

Deposited unit
A: Dual specificity protein kinase TTK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,04010
Polymers36,7271
Non-polymers1,3139
Water46826
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)76,07920
Polymers73,4542
Non-polymers2,62518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area1850 Å2
ΔGint-15 kcal/mol
Surface area23050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.470, 106.070, 112.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 36727.168 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 516-820
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTK, MPS1, MPS1L1 / Production host: Cell-free Synthesis (others) / References: UniProt: P33981, dual-specificity kinase
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-O22 / 4-[(4-amino-5-cyano-6-ethoxypyridin-2-yl)amino]benzamide


Mass: 297.312 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H15N5O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.89 Å3/Da / Density % sol: 57.47 % / Mosaicity: 0.8 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M MES pH 6, 13.8% w/v PEG 4000, 0.3M ammonium iodide, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 13, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.4→77.04 Å / Num. all: 17032 / Num. obs: 17032 / % possible obs: 100 % / Redundancy: 5.6 % / Rsym value: 0.073 / Net I/σ(I): 12.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.4-2.535.70.6920.5741.21390824410.2830.6920.5742.7100
2.53-2.685.70.5190.4291.71316923170.2130.5190.4293.8100
2.68-2.875.70.3390.2762.61249721950.1390.3390.2765.5100
2.87-3.15.70.2130.1714.31148620270.0880.2130.1718.4100
3.1-3.395.70.1350.1066.71083419150.0560.1350.10612.9100
3.39-3.795.60.0850.06410.6947116900.0350.0850.06419.3100
3.79-4.385.60.0690.0512.7849215150.0290.0690.0525.2100
4.38-5.375.50.0650.04413.9725713080.0270.0650.04427.1100
5.37-7.595.50.0710.03915.1559110240.030.0710.03924.7100
7.59-39.8124.80.0650.0412.928526000.0290.0650.0428.599.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å35.74 Å
Translation3 Å35.74 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.15data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.909 / WRfactor Rfree: 0.2843 / WRfactor Rwork: 0.2455 / Occupancy max: 1 / Occupancy min: 0.42 / FOM work R set: 0.8032 / SU B: 7.613 / SU ML: 0.181 / SU R Cruickshank DPI: 0.3365 / SU Rfree: 0.2613 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.336 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2844 1719 10.1 %RANDOM
Rwork0.2468 ---
obs0.2506 16997 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 93.07 Å2 / Biso mean: 51.9645 Å2 / Biso min: 24.92 Å2
Baniso -1Baniso -2Baniso -3
1--3.31 Å20 Å20 Å2
2--2.65 Å20 Å2
3---0.67 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2029 0 30 26 2085
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222095
X-RAY DIFFRACTIONr_angle_refined_deg1.0491.9742840
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7365254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.22325.22290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.88215360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.485156
X-RAY DIFFRACTIONr_chiral_restr0.0740.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211565
X-RAY DIFFRACTIONr_mcbond_it1.1711.51287
X-RAY DIFFRACTIONr_mcangle_it2.14922080
X-RAY DIFFRACTIONr_scbond_it2.8973808
X-RAY DIFFRACTIONr_scangle_it4.6524.5760
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 113 -
Rwork0.294 1115 -
all-1228 -
obs--100 %

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