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

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Basic information

Entry
Database: PDB / ID: 4usd
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 / 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-R09 / Serine/threonine-protein kinase 10
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.05 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
Revision 1.4Sep 19, 2018Group: Data collection / Category: diffrn_radiation_wavelength / diffrn_source
Item: _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list
Revision 1.5May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
Water00
1
A: SERINE/THREONINE-PROTEIN KINASE 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7822
Polymers34,2991
Non-polymers4841
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SERINE/THREONINE-PROTEIN KINASE 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7822
Polymers34,2991
Non-polymers4841
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.720, 99.600, 151.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 500
2111B1 - 500

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.993296, -0.11559, 0.001644), (-0.115546, -0.993159, -0.016845), (0.00358, 0.016542, -0.999857)0.09324, 3.54366, 7.58915

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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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Mar 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1

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Processing

SoftwareName: REFMAC / Version: 5.8.0073 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 3.05→83.41 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.898 / SU B: 65.069 / SU ML: 0.509 / Cross valid method: THROUGHOUT / ESU R Free: 0.539 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28863 632 4.9 %RANDOM
Rwork0.23447 ---
obs0.237 12247 91.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 81.98 Å2
Baniso -1Baniso -2Baniso -3
1-2.78 Å20 Å20 Å2
2---0.94 Å20 Å2
3----1.84 Å2
Refinement stepCycle: LAST / Resolution: 3.05→83.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4104 0 70 0 4174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194269
X-RAY DIFFRACTIONr_bond_other_d0.0020.024070
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.9995818
X-RAY DIFFRACTIONr_angle_other_deg0.8313.0039356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7675528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.90125.03169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.4515703
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1371516
X-RAY DIFFRACTIONr_chiral_restr0.0680.2667
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214724
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02876
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_it2.0733.8342133
X-RAY DIFFRACTIONr_mcbond_other2.0733.8322132
X-RAY DIFFRACTIONr_mcangle_it3.5725.7352654
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9724.1162136
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
Refine LS restraints NCSNumber: 4097 / Type: tight thermal / Rms dev position: 3.68 Å / Weight position: 0.5
LS refinement shellResolution: 3.05→3.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 48 -
Rwork0.367 856 -
obs--87.01 %
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)
115.116-3.09851.15094.25032.617914.8913-0.01211.13040.768-0.9484-0.25640.0874-2.2610.47660.26860.6574-0.0363-0.00230.13750.13150.210227.04610.652-11.953
23.2601-4.8542.02027.4686-2.49859.90990.26740.2217-0.355-0.5404-0.35970.8532-0.3972-1.11850.09230.51930.0271-0.19980.54810.01160.493918.3745.78-13.958
34.97680.98251.36744.9341.84957.76980.20640.850.1469-0.1119-0.14050.46960.5840.0172-0.06590.35140.0382-0.04110.1808-0.02060.088923.661-10.942-10.663
43.02880.7651.02573.62211.15387.05090.17370.637-0.4420.0011-0.06240.33161.48050.1179-0.11120.61750.1282-0.1730.1964-0.15770.28723.175-20.286-17.712
513.03931.76394.031512.26833.576211.39440.6915-1.5366-0.48741.2623-0.82780.45342.385-0.29860.13630.606-0.11690.0870.27740.08780.202525.666-10.57519.6
65.7133-1.7565-0.30448.41451.07816.2682-0.2234-0.8084-0.8760.5621-0.23742.121.4724-0.970.46080.6367-0.23950.22790.5778-0.06690.586617.902-4.75621.539
75.46580.12-1.84837.4412.898112.06280.142-0.6028-0.1602-0.1181-0.45220.7876-0.7696-0.5350.31010.11680.0176-0.00860.1346-0.0270.097625.03411.418.413
84.75290.3417-1.88795.26260.545210.79950.4379-0.60220.31910.0748-0.30280.5738-2.071-0.1603-0.13510.5167-0.06150.06960.1801-0.13030.176625.45320.55225.724
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 70
2X-RAY DIFFRACTION2A71 - 112
3X-RAY DIFFRACTION3A113 - 182
4X-RAY DIFFRACTION4A183 - 317
5X-RAY DIFFRACTION5B1 - 70
6X-RAY DIFFRACTION6B71 - 112
7X-RAY DIFFRACTION7B113 - 182
8X-RAY DIFFRACTION8B183 - 317

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