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- PDB-5vcw: CRYSTAL STRUCTURE OF HUMAN MYT1 KINASE DOMAIN IN COMPLEX WITH Pel... -

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Basic information

Entry
Database: PDB / ID: 5vcw
TitleCRYSTAL STRUCTURE OF HUMAN MYT1 KINASE DOMAIN IN COMPLEX WITH Pelitinib
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 / mitotic cell cycle ...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 / mitotic cell cycle / kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / Golgi membrane / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / nucleolus / Golgi apparatus / endoplasmic reticulum / nucleoplasm / ATP binding / membrane / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Tyrosine/threonine-protein kinase, Cdc2 inhibitor / 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 ...Tyrosine/threonine-protein kinase, Cdc2 inhibitor / 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-93J / 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: 2.25 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: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_validate_symm_contact / struct_conn
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
B: Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,66113
Polymers68,9962
Non-polymers1,66411
Water93752
1
A: Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2486
Polymers34,4981
Non-polymers7505
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4127
Polymers34,4981
Non-polymers9146
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.510, 112.900, 72.710
Angle α, β, γ (deg.)90.000, 109.270, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 34498.133 Da / Num. of mol.: 2 / 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
#2: Chemical ChemComp-93J / (2E)-N-{4-[(3-chloro-4-fluorophenyl)amino]-3-cyano-7-ethoxyquinolin-6-yl}-4-(dimethylamino)but-2-enamide


Mass: 467.923 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H23ClFN5O2
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.84 Å3/Da / Density % sol: 56.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 6.9 MG/ML MYT1, 25 mM HEPES, 100 MM SODIUM CHLORIDE, 0.5 mM DTT, 0.05 M MES pH 6.5, 0.8 M Magnesium sulfate, 2 mM Pelitinib

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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: Aug 25, 2014
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: 2.25→36.425 Å / Num. obs: 36183 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.426 % / Biso Wilson estimate: 43.2 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.076 / Rrim(I) all: 0.091 / Χ2: 0.974 / Net I/σ(I): 10.29
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.25-2.313.4250.3023.8526790.950.35799.4
2.31-2.373.4170.2574.425990.960.30399.2
2.37-2.443.4330.2065.2325390.9690.24499.4
2.44-2.523.4270.1795.9225020.9750.21199.9
2.52-2.63.4140.1576.6623690.9770.18599.5
2.6-2.693.4350.137.5423470.9860.15499.4
2.69-2.793.4350.1198.2322170.9860.14199.5
2.79-2.93.4230.1069.2321330.9870.12599.6
2.9-3.033.4160.09210.5320860.9860.10999.5
3.03-3.183.4260.08212.1119810.9890.09699.4
3.18-3.353.4380.07413.6418800.9910.08799.2
3.35-3.563.4180.06714.9417560.9910.0899.5
3.56-3.83.4350.06915.8516560.990.08198.9
3.8-4.113.4410.06816.5815510.9890.0898.4
4.11-4.53.4320.06717.0314070.9890.07997.8
4.5-5.033.4450.06717.1212860.990.07997.4
5.03-5.813.4530.06917.2811160.9870.08197.5
5.81-7.123.4680.06917.369470.9870.08196
7.12-10.063.3740.06717.437360.9840.0895.7
10.06-36.4253.2350.07516.893960.9890.0992.7

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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: 2.25→36.425 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.59
RfactorNum. reflection% reflection
Rfree0.2457 1194 3.3 %
Rwork0.1956 --
obs-36170 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 284.03 Å2 / Biso mean: 69.7286 Å2 / Biso min: 31.25 Å2
Refinement stepCycle: final / Resolution: 2.25→36.425 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4412 0 107 52 4571
Biso mean--74.68 53.33 -
Num. residues----570
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014667
X-RAY DIFFRACTIONf_angle_d1.2356320
X-RAY DIFFRACTIONf_chiral_restr0.048652
X-RAY DIFFRACTIONf_plane_restr0.006835
X-RAY DIFFRACTIONf_dihedral_angle_d15.9171748
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 (%)
2.2501-2.34010.35071330.25793886401999
2.3401-2.44660.31451330.23463897403099
2.4466-2.57560.3061330.227238874020100
2.5756-2.73690.31751330.224838984031100
2.7369-2.94810.28781330.226639014034100
2.9481-3.24460.3141320.217738764008100
3.2446-3.71370.25561340.19043912404699
3.7137-4.67740.18111320.16093867399998
4.6774-36.43010.21931310.17463852398396
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)
11.84991.2451-1.64972.189-1.2422.8604-0.12440.0137-0.3113-0.2314-0.1145-0.49920.48280.28590.24460.73480.07950.03460.40190.04990.485123.256618.72786.2422
24.9916-1.93391.14311.52310.62.10130.13390.44910.584-0.5542-0.0961-0.3841-0.2543-0.2817-0.02681.0280.1160.13320.40580.09030.490411.905234.0219.7209
33.8304-0.3959-0.58914.2968-0.75795.33450.4973-0.23640.15860.7235-0.18790.5143-0.2177-0.1491-0.18960.9061-0.02120.09230.383-0.01580.39334.032527.455224.0059
42.3702-0.96880.77710.427-0.71885.1-0.10720.07510.014-0.617-0.4720.8490.0251-0.7965-2.18580.71020.1272-0.49340.681-0.39151.048-13.124-10.8427-0.4582
51.4761-0.39911.90610.1233-0.56213.018-0.5320.04940.3242-0.5869-0.10241.1382-1.4699-0.16620.27861.09670.0406-0.43430.4158-0.03330.99670.4427-0.23612.952
62.4546-1.33970.33586.86910.05110.9019-0.33090.33650.2777-1.0762-0.0460.46-0.8036-0.4096-0.05980.56230.0132-0.18730.3178-0.02370.4676-0.4881-12.00292.9305
71.78360.51641.75824.21691.32872.9432-0.0795-0.13940.23640.4094-0.25490.7309-0.2293-0.23710.36930.57960.06920.07540.3257-0.04070.33966.1661-8.481218.58
84.6405-0.2935-0.63199.34821.89214.82080.06780.4443-0.9762-0.36370.00660.70640.5077-0.2714-0.03780.7329-0.0584-0.05860.4409-0.04780.62958.1822-24.080411.538
92.18733.4551-0.44077.71590.44872.0497-0.04410.3150.0355-0.38920.22910.42930.13740.4517-0.20880.85080.0914-0.02350.49020.01790.314620.1663-22.526314.9014
100.7648-0.6982-1.30855.95652.30084.74080.1197-0.05540.09860.70770.207-1.0807-0.23410.6283-0.33920.66010.0399-0.11440.40190.00460.421525.47-13.354722.4062
115.58371.9702-0.70693.36362.34026.97020.1682-0.0999-0.11051.199-0.06420.01620.1809-0.34730.00561.06860.0515-0.00680.39770.0470.353816.7-18.376632.2764
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 77 through 249 )A77 - 249
2X-RAY DIFFRACTION2chain 'A' and (resid 250 through 284 )A250 - 284
3X-RAY DIFFRACTION3chain 'A' and (resid 285 through 361 )A285 - 361
4X-RAY DIFFRACTION4chain 'B' and (resid 77 through 104 )B77 - 104
5X-RAY DIFFRACTION5chain 'B' and (resid 105 through 129 )B105 - 129
6X-RAY DIFFRACTION6chain 'B' and (resid 130 through 163 )B130 - 163
7X-RAY DIFFRACTION7chain 'B' and (resid 164 through 249 )B164 - 249
8X-RAY DIFFRACTION8chain 'B' and (resid 250 through 269 )B250 - 269
9X-RAY DIFFRACTION9chain 'B' and (resid 270 through 284 )B270 - 284
10X-RAY DIFFRACTION10chain 'B' and (resid 285 through 329 )B285 - 329
11X-RAY DIFFRACTION11chain 'B' and (resid 330 through 361 )B330 - 361

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