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- PDB-5vcy: CRYSTAL STRUCTURE OF HUMAN MYT1 KINASE DOMAIN IN COMPLEX WITH BOS... -

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Basic information

Entry
Database: PDB / ID: 5vcy
TitleCRYSTAL STRUCTURE OF HUMAN MYT1 KINASE DOMAIN IN COMPLEX WITH BOSUTINIB
ComponentsMembrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / KINASE DOMAIN / CELL CYCLE / TYROSINE- AND THREONINE-SPECIFIC KINASE / MEMBRANE-ASSOCIATED PROTEIN KINASE / TRANSFERASE / INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


negative regulation of G2/MI transition of meiotic cell cycle / G2/M DNA replication checkpoint / negative regulation of G2/M transition of mitotic cell cycle / Polo-like kinase mediated events / regulation of mitotic nuclear division / regulation of cyclin-dependent protein serine/threonine kinase activity / Cyclin A/B1/B2 associated events during G2/M transition / meiotic cell cycle / G2/M transition of mitotic cell cycle / kinase activity ...negative regulation of G2/MI transition of meiotic cell cycle / G2/M DNA replication checkpoint / negative regulation of G2/M transition of mitotic cell cycle / Polo-like kinase mediated events / regulation of mitotic nuclear division / regulation of cyclin-dependent protein serine/threonine kinase activity / Cyclin A/B1/B2 associated events during G2/M transition / meiotic cell cycle / G2/M transition of mitotic cell cycle / kinase activity / mitotic cell cycle / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / Rho-dependent protein serine/threonine kinase activity / ribosomal protein S6 kinase activity / histone H2BS14 kinase activity / histone H3T6 kinase activity / histone H3T45 kinase activity / histone H3S10 kinase activity / histone H3T11 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / Golgi membrane / protein serine/threonine kinase activity / protein serine kinase activity / endoplasmic reticulum membrane / nucleolus / Golgi apparatus / endoplasmic reticulum / nucleoplasm / ATP binding / nucleus / membrane / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Tyrosine/threonine-protein kinase, Cdc2 inhibitor / : / 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
Similarity search - Domain/homology
Chem-DB8 / DI(HYDROXYETHYL)ETHER / Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.56 Å
AuthorsZhu, J.-Y. / Schonbrunn, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)UO1 HD076542 United States
CitationJournal: J. Med. Chem. / Year: 2017
Title: Structural Basis of Wee Kinases Functionality and Inactivation by Diverse Small Molecule Inhibitors.
Authors: Zhu, J.Y. / Cuellar, R.A. / Berndt, N. / Lee, H.E. / Olesen, S.H. / Martin, M.P. / Jensen, J.T. / Georg, G.I. / Schonbrunn, E.
History
DepositionApr 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3997
Polymers34,4981
Non-polymers9016
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint11 kcal/mol
Surface area15140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.630, 55.000, 113.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase / Myt1 kinase


Mass: 34498.133 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, UNP RESIDUES 75-362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKMYT1, MYT1 / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)-RIPL
References: UniProt: Q99640, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 243 molecules

#2: Chemical ChemComp-DB8 / 4-[(2,4-dichloro-5-methoxyphenyl)amino]-6-methoxy-7-[3-(4-methylpiperazin-1-yl)propoxy]quinoline-3-carbonitrile / Bosutinib


Mass: 530.446 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H29Cl2N5O3 / Comment: inhibitor, medication*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.11 Å3/Da / Density % sol: 41.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 14 MG/ML MYT1, 50 mM HEPES PH 7.5, 0.5 mM DTT, 0.05 M POTASSIUM CHLORIDE, 17.5 (V/V) % pentaerythritol propoxylate (5/4 PO/OH), 1.5 mM BOSUTINIB

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 19, 2016
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.56→36.048 Å / Num. obs: 41721 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 2.833 % / Biso Wilson estimate: 15.19 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.059 / Χ2: 0.957 / Net I/σ(I): 13.94
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.56-1.62.8240.3582.8630730.80.44498.9
1.6-1.642.8270.3193.2729490.8510.39598.8
1.64-1.692.8210.2633.9328890.890.32598.8
1.69-1.742.8270.2074.9628410.9290.25699.1
1.74-1.82.8150.1636.2327560.9510.20299.3
1.8-1.862.8150.1347.4226640.9720.16699.6
1.86-1.932.8180.19.5525780.9810.12499.6
1.93-2.012.830.08311.6324800.9870.10299.3
2.01-2.12.8230.06314.2923790.9930.07799.3
2.1-2.212.830.05316.5522990.9950.06699.3
2.21-2.332.8370.04918.4721740.9950.06199.2
2.33-2.472.8290.04519.9220350.9950.05599
2.47-2.642.8270.04122.1819320.9960.05198.3
2.64-2.852.8570.03923.7618010.9960.04798.3
2.85-3.122.8670.03526.7216490.9960.04397.3
3.12-3.492.8590.03129.8814850.9970.03896.5
3.49-4.032.8720.0331.8413110.9970.03795.6
4.03-4.932.8840.02932.6711040.9970.03693.8
4.93-6.982.8760.03131.738610.9970.03892.2
6.98-36.0482.8130.02933.094610.9960.03683.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
SERGUIdata collection
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VCV

5vcv


Resolution: 1.56→36.048 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.08
RfactorNum. reflection% reflection
Rfree0.1778 1252 3 %
Rwork0.1397 --
obs-41719 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 127.53 Å2 / Biso mean: 25.3139 Å2 / Biso min: 8.15 Å2
Refinement stepCycle: final / Resolution: 1.56→36.048 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2302 0 122 237 2661
Biso mean--36.99 29.63 -
Num. residues----296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072446
X-RAY DIFFRACTIONf_angle_d1.1793307
X-RAY DIFFRACTIONf_chiral_restr0.043340
X-RAY DIFFRACTIONf_plane_restr0.006437
X-RAY DIFFRACTIONf_dihedral_angle_d14.751923
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5599-1.62240.22431370.16284442457999
1.6224-1.69620.24041370.15214433457099
1.6962-1.78560.19521390.13734494463399
1.7856-1.89750.19711400.123745164656100
1.8975-2.0440.16551390.11684504464399
2.044-2.24970.15191400.11834524466499
2.2497-2.57510.17641410.1334541468299
2.5751-3.24410.19421390.15014507464698
3.2441-36.05790.16591400.15114506464693

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