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- PDB-6i2y: Human STK10 bound to Foretinib -

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Basic information

Entry
Database: PDB / ID: 6i2y
TitleHuman STK10 bound to Foretinib
ComponentsSerine/threonine-protein kinase 10
KeywordsTRANSFERASE / kinase / inhibitor / complex / LOK / foretinib
Function / homology
Function and homology information


lymphocyte aggregation / regulation of lymphocyte migration / RHOB GTPase cycle / RHOC GTPase cycle / RHOA GTPase cycle / specific granule membrane / protein autophosphorylation / non-specific serine/threonine protein kinase / cell cycle / protein phosphorylation ...lymphocyte aggregation / regulation of lymphocyte migration / RHOB GTPase cycle / RHOC GTPase cycle / RHOA GTPase cycle / specific granule membrane / protein autophosphorylation / non-specific serine/threonine protein kinase / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / Neutrophil degranulation / protein homodimerization activity / extracellular exosome / ATP binding / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Serine/threonine-protein kinase 10, catalytic domain / Polo kinase kinase / Polo kinase kinase / 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 kinase 10, catalytic domain / Polo kinase kinase / Polo kinase kinase / 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-88Z / Serine/threonine-protein kinase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsSorrell, F.J. / Berger, B.-T. / Oerum, S. / von Delft, F. / Bountra, C. / Arrowsmith, C. / Edwards, A.M. / Knapp, S. / Elkins, J.M.
CitationJournal: To Be Published
Title: Human STK10 bound to GW683134
Authors: Sorrell, F.J. / Elkins, J.M.
History
DepositionNov 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase 10
B: Serine/threonine-protein kinase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7464
Polymers68,4812
Non-polymers1,2652
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Disulfide bond between two cysteines in asymmetric unit.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-25 kcal/mol
Surface area26780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.930, 95.330, 132.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 24 and (name N or name...
21(chain B and (resid 24 through 79 or (resid 80...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and ((resid 24 and (name N or name...A24
121(chain A and ((resid 24 and (name N or name...A24 - 317
131(chain A and ((resid 24 and (name N or name...A24 - 317
141(chain A and ((resid 24 and (name N or name...A24 - 317
151(chain A and ((resid 24 and (name N or name...A24 - 317
211(chain B and (resid 24 through 79 or (resid 80...B24 - 79
221(chain B and (resid 24 through 79 or (resid 80...B80
231(chain B and (resid 24 through 79 or (resid 80...B24 - 317
241(chain B and (resid 24 through 79 or (resid 80...B24 - 317
251(chain B and (resid 24 through 79 or (resid 80...B24 - 317
261(chain B and (resid 24 through 79 or (resid 80...B24 - 317

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Components

#1: Protein Serine/threonine-protein kinase 10 / Lymphocyte-oriented kinase


Mass: 34240.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STK10, LOK / Production host: Escherichia coli (E. coli)
References: UniProt: O94804, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-88Z / N-(3-fluoro-4-{[6-methoxy-7-(3-morpholin-4-ylpropoxy)quinolin-4-yl]oxy}phenyl)-N'-(4-fluorophenyl)cyclopropane-1,1-dicarboxamide


Mass: 632.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34F2N4O6 / Feature type: SUBJECT OF INVESTIGATION

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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: 2.35 Å3/Da / Density % sol: 47.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2M sodium chloride -- 25% PEG3350 -- 0.1M bis-tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.56→54.5 Å / Num. obs: 21454 / % possible obs: 99.4 % / Redundancy: 6.3 % / Biso Wilson estimate: 67.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.039 / Rrim(I) all: 0.098 / Net I/σ(I): 11.2 / Num. measured all: 135087
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.56-2.635.81.501885015340.6680.6831.6521.199.4
11.45-54.550.03114952970.9980.0140.03534.898

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.27data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.56→54.502 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 39.73
RfactorNum. reflection% reflection
Rfree0.2828 1011 4.73 %
Rwork0.263 --
obs0.2639 21389 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 194.33 Å2 / Biso mean: 102.9504 Å2 / Biso min: 39.24 Å2
Refinement stepCycle: final / Resolution: 2.56→54.502 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4047 0 92 0 4139
Biso mean--80.87 --
Num. residues----556
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034234
X-RAY DIFFRACTIONf_angle_d0.6745800
X-RAY DIFFRACTIONf_chiral_restr0.046677
X-RAY DIFFRACTIONf_plane_restr0.006804
X-RAY DIFFRACTIONf_dihedral_angle_d17.982564
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2250X-RAY DIFFRACTION15.593TORSIONAL
12B2250X-RAY DIFFRACTION15.593TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5601-2.6950.48931490.455128422991
2.695-2.86390.40721410.40728603001
2.8639-3.0850.37711460.35228643010
3.085-3.39540.32481420.304828813023
3.3954-3.88660.30531390.276329023041
3.8866-4.89620.23461410.219529353076
4.8962-54.51460.23171530.221730943247
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)
10.117-0.0994-0.04750.6638-0.25020.1850.3691-0.0617-0.3431-0.0938-0.65070.26470.4904-0.3037-1.15071.297-0.86020.35640.0845-0.11592.17975.8959-24.82880.3939
20.5194-0.63990.46930.9499-0.83190.59910.38660.1483-0.58270.474-0.0408-0.5674-0.07820.30160.00010.74530.0653-0.12470.6822-0.1281.02621.0862-20.5726-2.7441
30.3076-0.4177-0.40571.06260.16450.4282-0.24120.470.43740.0786-0.1315-0.63550.40870.14910.03740.55760.05030.00170.76470.01130.8228.3306-14.4325.2263
42.27420.24530.9830.9092-0.00272.7911-0.10830.6495-0.0672-0.1602-0.01320.3164-0.8502-0.5834-0.15760.63350.0342-0.01550.57640.00140.569714.4181-3.1569-4.6649
56.83461.47841.83120.7690.57130.5827-0.18922.6131-0.7686-0.54460.7147-0.5972-0.72570.40940.12260.45980.1455-0.1379-0.01870.14230.480316.0273-1.085-4.5879
61.12741.3075-1.32111.1256-1.05545.42640.0830.4463-0.1703-1.10851.0451-0.210.726-1.68610.4197-0.02420.4289-0.16790.11340.18560.34718.0109-4.33222.6833
70.89260.7609-0.21860.6092-0.13650.18330.9415-1.2405-0.19690.5457-0.78660.1282-0.7254-0.00660.02710.87840.1283-0.0411.1625-0.05070.7945-10.04888.500920.4916
81.27140.0411.50980.26480.00121.658-0.9772-1.15860.35420.81970.6704-0.1143-1.8395-0.6282-0.26161.40840.3384-0.26240.56570.01260.838613.26169.3062.1369
93.29180.24490.81420.6243-0.27671.0424-0.2049-1.61990.715-0.3989-0.307-0.0841-1.0653-0.626-0.65611.75350.5684-0.39820.7432-0.24080.987413.530716.57944.5921
100.0326-0.0743-0.18410.77890.36182.5358-0.40.02590.4405-0.31460.2085-0.3671-1.16240.3987-0.02530.84810.0813-0.15820.91550.2190.688119.08696.0861-12.8961
110.19540.0052-0.08680.2240.30570.60240.4685-0.5112-2.2043-0.81440.3922-0.62381.0283-0.68660.88841.1915-0.02-0.1890.93710.48551.7141-17.4967-18.966735.1678
122.2764-2.3396-0.24172.1430.09950.2075-0.7405-0.3038-1.031-0.21051.57540.41562.00640.97610.34021.1922-0.3639-0.09561.47940.19580.9478-18.0948-17.224535.8316
130.20370.0482-0.20320.37360.4960.4968-0.69050.2022-0.54180.56820.57650.43190.61451.3286-0.00860.7384-0.1632-0.06521.1706-0.20360.7895-5.7043-9.087835.345
140.6656-0.4233-0.45090.31060.76150.83580.2533-0.30650.17270.5315-0.41690.2363-0.3747-0.93960.20630.5741-0.0678-0.0931.2916-0.01990.6185-19.8755-3.156739.3344
151.3571-0.53221.0992.04890.58811.08110.1099-0.26230.0112-0.27530.3118-0.2281-0.27970.0453-0.00020.6603-0.08990.00521.0926-0.15390.6959-9.85521.450338.2251
164.2506-2.8961.41781.9768-0.83681.18330.62131.08050.61831.3471-0.6265-0.6354-1.0053-0.817-0.45051.04780.0702-0.11190.3973-0.10530.650413.16924.401812.7216
174.01032.25350.1681.26880.10030.01351.0645-0.8053-2.2063-0.8454-2.1691.2151-0.0981-1.1051-0.06941.75580.40120.0041.2950.04470.96275.22028.418318.7452
180.17560.05190.25250.0554-0.14070.4645-0.38520.33580.784-0.15240.4263-0.2741-0.3327-1.079300.7590.07520.0291.3378-0.05820.7282-12.560511.376732.8777
190.4346-0.1078-0.18321.43810.92790.8083-0.00940.01410.3175-0.49810.0255-0.1795-0.42520.0044-0.00020.8535-0.09630.02920.8971-0.02790.6958-12.186117.200233.305
200.12830.1284-0.18080.26280.40690.25640.2080.45820.8248-0.0404-0.19820.1798-0.5048-0.84210.00010.69310.07160.12921.1848-0.1590.7659-29.45942.670448.2574
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 24:28)A24 - 28
2X-RAY DIFFRACTION2(chain A and resid 29:62)A29 - 62
3X-RAY DIFFRACTION3(chain A and resid 63:90)A63 - 90
4X-RAY DIFFRACTION4(chain A and resid 91:155)A91 - 155
5X-RAY DIFFRACTION5(chain A and resid 156:170)A156 - 170
6X-RAY DIFFRACTION6(chain A and resid 171:193)A171 - 193
7X-RAY DIFFRACTION7(chain A and resid 194:214)A194 - 214
8X-RAY DIFFRACTION8(chain A and resid 215:235)A215 - 235
9X-RAY DIFFRACTION9(chain A and resid 236:285)A236 - 285
10X-RAY DIFFRACTION10(chain A and resid 286:317)A286 - 317
11X-RAY DIFFRACTION11(chain B and resid 24:49)B24 - 49
12X-RAY DIFFRACTION12(chain B and resid 50:74)B50 - 74
13X-RAY DIFFRACTION13(chain B and resid 75:95)B75 - 95
14X-RAY DIFFRACTION14(chain B and resid 96:136)B96 - 136
15X-RAY DIFFRACTION15(chain B and resid 137:181)B137 - 181
16X-RAY DIFFRACTION16(chain B and resid 182:199)B182 - 199
17X-RAY DIFFRACTION17(chain B and resid 200:215)B200 - 215
18X-RAY DIFFRACTION18(chain B and resid 216:233)B216 - 233
19X-RAY DIFFRACTION19(chain B and resid 234:300)B234 - 300
20X-RAY DIFFRACTION20(chain B and resid 301:317)B301 - 317

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