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- PDB-6hxf: Human STK10 bound to a maleimide inhibitor -

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Basic information

Entry
Database: PDB / ID: 6hxf
TitleHuman STK10 bound to a maleimide inhibitor
ComponentsSerine/threonine-protein kinase 10
KeywordsTRANSFERASE / Kinase
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 / protein phosphorylation / protein serine kinase activity ...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 / 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 / cytosol / cytoplasm
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. ...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-R70 / Serine/threonine-protein kinase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.09 Å
AuthorsSorrell, F.J. / Salah, E. / Serafim, R.A.M. / Savitsky, P.A. / Krojer, T. / Bailey, H.J. / Pinkas, D. / Burgess-Brown, N.A. / von Delft, F. / Knapp, S. ...Sorrell, F.J. / Salah, E. / Serafim, R.A.M. / Savitsky, P.A. / Krojer, T. / Bailey, H.J. / Pinkas, D. / Burgess-Brown, N.A. / von Delft, F. / Knapp, S. / Arrowsmith, C. / Bountra, C. / Edwards, A.M. / Elkins, J.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: To Be Published
Title: Human STK10 bound to a maleimide inhibitor
Authors: Sorrell, F.J. / Salah, E. / Serafim, R.A.M. / Elkins, J.M.
History
DepositionOct 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)140,28017
Polymers138,1544
Non-polymers2,12613
Water13,061725
1
B: Serine/threonine-protein kinase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1856
Polymers34,5391
Non-polymers6475
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Serine/threonine-protein kinase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9723
Polymers34,5391
Non-polymers4342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Serine/threonine-protein kinase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9993
Polymers34,5391
Non-polymers4602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Serine/threonine-protein kinase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1235
Polymers34,5391
Non-polymers5854
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.840, 101.670, 198.000
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 25 or (resid 26...
31(chain C and ((resid 24 and (name N or name...
41(chain D and (resid 24 through 25 or (resid 26...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUGLUGLU(chain A and ((resid 24 and (name N or name...AB249
12GLUGLUGLUGLU(chain A and ((resid 24 and (name N or name...AB24 - 3139 - 298
13GLUGLUGLUGLU(chain A and ((resid 24 and (name N or name...AB24 - 3139 - 298
14GLUGLUGLUGLU(chain A and ((resid 24 and (name N or name...AB24 - 3139 - 298
15GLUGLUGLUGLU(chain A and ((resid 24 and (name N or name...AB24 - 3139 - 298
21GLUGLUHISHIS(chain B and (resid 24 through 25 or (resid 26...BA24 - 259 - 10
22VALVALARGARG(chain B and (resid 24 through 25 or (resid 26...BA26 - 2811 - 13
23GLUGLUVALVAL(chain B and (resid 24 through 25 or (resid 26...BA24 - 3149 - 299
24GLUGLUVALVAL(chain B and (resid 24 through 25 or (resid 26...BA24 - 3149 - 299
25GLUGLUVALVAL(chain B and (resid 24 through 25 or (resid 26...BA24 - 3149 - 299
26GLUGLUVALVAL(chain B and (resid 24 through 25 or (resid 26...BA24 - 3149 - 299
31GLUGLUGLUGLU(chain C and ((resid 24 and (name N or name...CC249
32GLUGLUALAALA(chain C and ((resid 24 and (name N or name...CC24 - 3129 - 297
33GLUGLUALAALA(chain C and ((resid 24 and (name N or name...CC24 - 3129 - 297
34GLUGLUALAALA(chain C and ((resid 24 and (name N or name...CC24 - 3129 - 297
35GLUGLUALAALA(chain C and ((resid 24 and (name N or name...CC24 - 3129 - 297
41GLUGLUHISHIS(chain D and (resid 24 through 25 or (resid 26...DD24 - 259 - 10
42VALVALARGARG(chain D and (resid 24 through 25 or (resid 26...DD26 - 2811 - 13
43TYRTYRALAALA(chain D and (resid 24 through 25 or (resid 26...DD23 - 3128 - 297
44TYRTYRALAALA(chain D and (resid 24 through 25 or (resid 26...DD23 - 3128 - 297
45TYRTYRALAALA(chain D and (resid 24 through 25 or (resid 26...DD23 - 3128 - 297
46TYRTYRALAALA(chain D and (resid 24 through 25 or (resid 26...DD23 - 3128 - 297

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Components

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


Mass: 34538.547 Da / Num. of mol.: 4
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-R70 / 3-(2-methoxyphenyl)-4-[[4-(phenylcarbonyl)phenyl]amino]pyrrole-2,5-dione


Mass: 398.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H18N2O4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 725 / 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: 3.48 Å3/Da / Density % sol: 64.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.10M MgCl2; 0.1M TRIS pH 8.0; 20.0% PEG 6K; 10.0% EtGly

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9195 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9195 Å / Relative weight: 1
ReflectionResolution: 2.09→65.452 Å / Num. obs: 113868 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 34.15 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.064 / Rrim(I) all: 0.166 / Net I/σ(I): 8.8
Reflection shellResolution: 2.09→2.14 Å / Redundancy: 6.4 % / Num. unique obs: 8335 / CC1/2: 0.579 / Rpim(I) all: 0.638 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.09 Å65.45 Å
Translation2.09 Å65.45 Å

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.7.17phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ajq

5ajq


Resolution: 2.09→65.452 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.23
RfactorNum. reflection% reflection
Rfree0.2191 5500 4.84 %
Rwork0.1903 --
obs0.1917 113731 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 138.59 Å2 / Biso mean: 49.7376 Å2 / Biso min: 18.67 Å2
Refinement stepCycle: final / Resolution: 2.09→65.452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8852 0 153 725 9730
Biso mean--43.03 48.58 -
Num. residues----1151
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2850X-RAY DIFFRACTION14.057TORSIONAL
12B2850X-RAY DIFFRACTION14.057TORSIONAL
13C2850X-RAY DIFFRACTION14.057TORSIONAL
14D2850X-RAY DIFFRACTION14.057TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.09-2.11380.34541800.293601
2.1138-2.13860.29151690.27383562
2.1386-2.16470.27141840.25353581
2.1647-2.19210.29261860.24763511
2.1921-2.2210.30451740.24143630
2.221-2.25140.24291680.2453577
2.2514-2.28360.27112020.23863545
2.2836-2.31760.26531720.22723593
2.3176-2.35390.27841690.22033554
2.3539-2.39240.27121830.21683605
2.3924-2.43370.23961530.21413586
2.4337-2.4780.271930.21073578
2.478-2.52560.24191930.20183576
2.5256-2.57720.24861660.19763584
2.5772-2.63320.20341680.19033596
2.6332-2.69450.25652030.1893558
2.6945-2.76190.21712140.18583555
2.7619-2.83650.20831910.19053595
2.8365-2.920.21091880.19513601
2.92-3.01420.20821820.18223609
3.0142-3.1220.22982160.18353549
3.122-3.2470.23551800.19233627
3.247-3.39470.24811680.18413665
3.3947-3.57370.21811870.18633581
3.5737-3.79760.21381660.17073676
3.7976-4.09080.16951710.15513648
4.0908-4.50230.18731680.14883688
4.5023-5.15360.18352090.16293647
5.1536-6.49210.1882113690
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)
16.7222-0.42762.18867.7731-0.4265.04150.2992-1.6399-0.54851.2114-0.1647-0.88990.27170.9648-0.2360.71750.0422-0.20391.12160.03620.6056-51.0154-10.514921.8841
23.7661-0.0082-1.06282.74550.36342.64710.1345-0.52610.47410.48990.1691-0.2798-0.07640.486-0.16670.3036-0.04160.01930.3726-0.10550.3865-60.3486-2.89549.9929
34.9003-0.7383-2.99993.73872.79285.65210.0174-0.022-0.17520.41210.0668-0.11470.48240.0738-0.04390.26890.00230.00620.23870.02560.3636-72.8742-11.94954.8371
42.3004-0.2-0.52422.02490.16712.25930.26370.32270.54580.05780.0120.1634-0.2854-0.2516-0.28040.24420.01880.09450.27170.06290.4437-79.259-1.16472.3359
56.93180.40581.08949.1489-5.61346.29690.4264-0.8591.61670.97590.4938-0.2348-1.34730.2939-0.61580.6055-0.08910.22830.5016-0.25831.0665-63.914114.409813.3279
61.97740.31151.1184.22530.37312.30290.52430.58230.6057-1.0766-0.2868-1.0673-1.05930.0644-0.26820.8839-0.18460.32761.2483-0.03860.738-7.93938.0793-24.1309
74.3133-1.9105-1.1353.97092.71817.3712-0.00371.42990.6568-1.10090.1784-1.1329-0.56130.05290.01390.5083-0.11640.20710.85470.07970.569-10.58289.4932-21.544
83.11860.40870.3582.34920.71781.5264-0.11350.4082-0.0483-0.33850.2764-0.4648-0.0840.3546-0.02540.2501-0.02190.05970.3867-0.0510.3575-17.6473.9897-9.2589
92.43090.2320.38991.76840.7562.5686-0.0412-0.15680.0871-0.05270.01180.0145-0.038-0.00850.03210.16050.00770.00020.2236-0.0110.2436-34.00324.7735-1.4639
109.4734-2.8272-3.89617.37913.39782.7663-0.18760.5374-1.0484-0.3115-0.1004-0.50640.82520.41120.07310.3860.030.0430.3017-0.05030.7299-21.3115-15.0825-9.6163
117.0363.239-2.14122.18370.31783.4695-0.20550.557-0.93590.0207-0.22610.53760.9948-0.6740.42060.8966-0.0760.07510.4474-0.15440.5382-56.585518.2717-44.9133
121.9088-0.1874-0.91651.48740.74714.4148-0.23520.2307-0.1919-0.4202-0.08460.13870.4438-0.20720.27610.4174-0.00720.01920.2784-0.00590.3054-58.418326.6522-32.3485
137.9134-0.6748-0.72680.1412-0.1690.80430.12450.5965-1.7411-0.02940.24550.20460.4575-0.746-0.25240.584-0.0501-0.09220.51680.01210.7153-56.914915.8313-14.1278
142.64950.04980.35873.20030.05431.8748-0.0225-0.1050.22990.0532-0.0648-0.16330.15120.04020.08670.22120.01670.01090.22260.00110.2501-52.017532.2804-11.9567
159.062-6.1676-5.8256.725.19654.58660.48130.46750.13-0.9708-0.26250.0282-1.0448-0.2928-0.18970.55230.0596-0.09920.2860.05490.412-56.614145.6214-29.5756
168.64211.8857-0.56515.26910.13815.4601-0.06270.4224-0.5228-0.2994-0.12410.23090.4478-0.3550.0910.5449-0.00440.00050.3039-0.04830.2526-55.267-30.8675-45.4109
174.44413.97-3.32614.3625-3.32462.6434-0.4079-1.7297-1.21291.2986-0.4854-1.08690.10230.43540.80291.11120.02240.11680.68860.19250.6143-54.0404-44.2428-35.8807
181.24930.79240.29893.28611.29713.2032-0.06440.12380.0227-0.4221-0.03580.09080.0343-0.14110.10860.23350.0094-0.02810.23420.01850.23-57.2048-22.7921-30.123
196.89831.7120.61495.45340.52763.85780.07930.1331-0.7634-0.106-0.0798-0.19090.7502-0.2076-0.06090.3937-0.0273-0.03020.27370.00130.3597-51.8773-31.7422-16.3743
201.79310.17590.34413.18380.33881.94720.01520.00110.2786-0.0966-0.0314-0.0287-0.048-0.01230.00830.2192-0.00480.00990.2385-0.0080.2586-49.7318-15.4576-15.5996
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 24:78)A24 - 78
2X-RAY DIFFRACTION2(chain A and resid 79:181)A79 - 181
3X-RAY DIFFRACTION3(chain A and resid 182:233)A182 - 233
4X-RAY DIFFRACTION4(chain A and resid 234:298)A234 - 298
5X-RAY DIFFRACTION5(chain A and resid 299:313)A299 - 313
6X-RAY DIFFRACTION6(chain B and resid 24:47)B24 - 47
7X-RAY DIFFRACTION7(chain B and resid 48:78)B48 - 78
8X-RAY DIFFRACTION8(chain B and resid 79:191)B79 - 191
9X-RAY DIFFRACTION9(chain B and resid 192:295)B192 - 295
10X-RAY DIFFRACTION10(chain B and resid 296:314)B296 - 314
11X-RAY DIFFRACTION11(chain C and resid 24:48)C24 - 48
12X-RAY DIFFRACTION12(chain C and resid 49:179)C49 - 179
13X-RAY DIFFRACTION13(chain C and resid 180:215)C180 - 215
14X-RAY DIFFRACTION14(chain C and resid 216:295)C216 - 295
15X-RAY DIFFRACTION15(chain C and resid 296:312)C296 - 312
16X-RAY DIFFRACTION16(chain D and resid 23:67)D23 - 67
17X-RAY DIFFRACTION17(chain D and resid 68:78)D68 - 78
18X-RAY DIFFRACTION18(chain D and resid 79:182)D79 - 182
19X-RAY DIFFRACTION19(chain D and resid 183:225)D183 - 225
20X-RAY DIFFRACTION20(chain D and resid 226:312)D226 - 312

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