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- PDB-4use: Human STK10 (LOK) with SB-633825 -

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Basic information

Entry
Database: PDB / ID: 4use
TitleHuman STK10 (LOK) with SB-633825
ComponentsSERINE/THREONINE-PROTEIN KINASE 10
KeywordsTRANSFERASE
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-R09 / Serine/threonine-protein kinase 10
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsElkins, J.M. / Salah, E. / Szklarz, M. / von Delft, F. / Canning, P. / Raynor, J. / Bountra, C. / Edwards, A.M. / Knapp, S.
CitationJournal: Nat.Biotechnol. / Year: 2016
Title: Comprehensive Characterization of the Published Kinase Inhibitor Set.
Authors: Elkins, J.M. / Fedele, V. / Szklarz, M. / Abdul Azeez, K.R. / Salah, E. / Mikolajczyk, J. / Romanov, S. / Sepetov, N. / Huang, X.P. / Roth, B.L. / Al Haj Zen, A. / Fourches, D. / Muratov, E. ...Authors: Elkins, J.M. / Fedele, V. / Szklarz, M. / Abdul Azeez, K.R. / Salah, E. / Mikolajczyk, J. / Romanov, S. / Sepetov, N. / Huang, X.P. / Roth, B.L. / Al Haj Zen, A. / Fourches, D. / Muratov, E. / Tropsha, A. / Morris, J. / Teicher, B.A. / Kunkel, M. / Polley, E. / Lackey, K.E. / Atkinson, F.L. / Overington, J.P. / Bamborough, P. / Moller, S. / Price, D.J. / Willson, T.M. / Drewry, D.H. / Knapp, S. / Zuercher, W.J.
History
DepositionJul 7, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Jan 20, 2016Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

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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)69,5644
Polymers68,5972
Non-polymers9672
Water28816
1
A: SERINE/THREONINE-PROTEIN KINASE 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7822
Polymers34,2991
Non-polymers4841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: SERINE/THREONINE-PROTEIN KINASE 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7822
Polymers34,2991
Non-polymers4841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)62.040, 50.250, 133.710
Angle α, β, γ (deg.)90.00, 101.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SERINE/THREONINE-PROTEIN KINASE 10 / LYMPHOCYTE-ORIENTED KINASE / STK10


Mass: 34298.605 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 18-317
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O94804, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-R09 / 4-{5-(6-methoxynaphthalen-2-yl)-1-methyl-2-[2-methyl-4-(methylsulfonyl)phenyl]-1H-imidazol-4-yl}pyridine


Mass: 483.581 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H25N3O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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 Å3/Da / Density % sol: 59 % / Description: NONE
Crystal growpH: 6.5
Details: 50% (V/V) PEG 300, 0.1M CACODYLATE PH 6.5, 0.2M MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Jul 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.65→65.59 Å / Num. obs: 23790 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 5.3
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 1.8 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 2.65→131.18 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.918 / SU B: 33.069 / SU ML: 0.306 / Cross valid method: THROUGHOUT / ESU R: 0.591 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25145 1192 5.1 %RANDOM
Rwork0.22454 ---
obs0.22598 22179 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.105 Å2
Baniso -1Baniso -2Baniso -3
1-4.08 Å20 Å22.79 Å2
2---3.11 Å20 Å2
3----1.92 Å2
Refinement stepCycle: LAST / Resolution: 2.65→131.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4284 0 70 16 4370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194461
X-RAY DIFFRACTIONr_bond_other_d0.0020.024241
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.9956087
X-RAY DIFFRACTIONr_angle_other_deg0.8263.0039737
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0965560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83724.85167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.47715726
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.631516
X-RAY DIFFRACTIONr_chiral_restr0.0680.2706
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214944
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02916
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6243.5042252
X-RAY DIFFRACTIONr_mcbond_other1.6193.5042251
X-RAY DIFFRACTIONr_mcangle_it2.8535.2522805
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1353.7312209
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 83 -
Rwork0.374 1486 -
obs--89.81 %
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)
19.76042.1195-1.99772.23771.07171.85620.0169-0.3354-0.54610.4527-0.51160.4720.236-0.62080.49470.45780.08270.08960.72510.13370.4108-6.82040.7536-55.1176
22.6056-1.45451.39957.14591.5864.6006-0.0806-0.07830.04850.2436-0.06290.50620.00830.03870.14350.1247-0.02630.03050.0142-0.01680.049913.48320.0822-55.1678
30.8461.73212.75954.84948.773816.6370.47230.09970.22921.3504-0.32260.02742.5002-1.179-0.14970.9614-0.2339-0.08040.6291-0.0460.417510.63117.0807-40.4548
41.91770.5370.63995.26831.75545.0611-0.0375-0.2040.08420.48510.1182-0.43160.00790.6369-0.08070.1110.0063-0.02570.1253-0.0180.051922.2036-0.0683-47.9762
50.62121.54151.23516.57765.04275.2812-0.14640.36330.602-0.9192-0.36191.0555-0.6749-0.71750.50831.10320.04010.13871.26290.35641.1729-13.5477-20.579-18.3488
64.29271.2028-1.96235.56380.06315.22590.00520.3779-0.0394-0.0433-0.06130.65050.0522-0.33940.05610.59520.03980.12230.0464-0.01460.11231.4957-21.7311-9.7021
72.3232-2.9505-3.45986.38448.757112.40660.4535-0.1627-0.2636-1.238-0.5990.1371-1.6489-1.08640.14560.86140.18410.16160.626-0.09710.38118.7996-27.4314-23.6715
82.4121-0.8729-1.72224.99721.76754.9168-0.0723-0.1675-0.1083-0.04040.1564-0.5706-0.00560.7741-0.08410.4597-0.00470.07220.1305-0.00740.092215.3369-20.6843-12.7668
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 112
2X-RAY DIFFRACTION2A113 - 188
3X-RAY DIFFRACTION3A189 - 216
4X-RAY DIFFRACTION4A217 - 316
5X-RAY DIFFRACTION5B34 - 89
6X-RAY DIFFRACTION6B90 - 188
7X-RAY DIFFRACTION7B189 - 217
8X-RAY DIFFRACTION8B218 - 316

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