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- PDB-5owq: Human STK10 bound to dovitinib -

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Basic information

Entry
Database: PDB / ID: 5owq
TitleHuman STK10 bound to dovitinib
ComponentsSerine/threonine-protein kinase 10
KeywordsTRANSFERASE / Kinase / Structural Genomics Consortium / SGC
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 / protein phosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction ...lymphocyte aggregation / regulation of lymphocyte migration / RHOB GTPase cycle / RHOC GTPase cycle / RHOA GTPase cycle / specific granule membrane / protein autophosphorylation / protein phosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / nuclear body / protein serine kinase activity / protein serine/threonine kinase activity / Neutrophil degranulation / protein homodimerization activity / extracellular exosome / nucleoplasm / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-38O / Serine/threonine-protein kinase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSzklarz, M. / von Delft, F. / Bountra, C. / Knapp, S. / Edwards, A.M. / Arrowsmith, C. / Elkins, J.M.
CitationJournal: To Be Published
Title: Human STK10 bound to dovitinib
Authors: Elkins, J.M.
History
DepositionSep 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.2May 1, 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)69,3824
Polymers68,5972
Non-polymers7852
Water00
1
A: Serine/threonine-protein kinase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6912
Polymers34,2991
Non-polymers3921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6912
Polymers34,2991
Non-polymers3921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-26 kcal/mol
Surface area25700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.570, 50.400, 114.570
Angle α, β, γ (deg.)90.00, 96.60, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 32 - 316 / Label seq-ID: 17 - 301

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 34298.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STK10, LOK / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3)
References: UniProt: O94804, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-38O / 4-amino-5-fluoro-3-[5-(4-methylpiperazin-1-yl)-1H-benzimidazol-2-yl]quinolin-2(1H)-one / Dovitinib


Mass: 392.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H21FN6O
Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 48.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1M sodium formate, 15%(w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.7→57.19 Å / Num. obs: 16619 / % possible obs: 91.4 % / Redundancy: 2.8 % / CC1/2: 0.984 / Rmerge(I) obs: 0.14 / Net I/σ(I): 4.7
Reflection shellResolution: 2.7→2.86 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2672 / CC1/2: 0.692 / % possible all: 91.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: STK10

Resolution: 2.7→57.19 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.879 / SU B: 50.88 / SU ML: 0.443 / Cross valid method: THROUGHOUT / ESU R: 6.612 / ESU R Free: 0.433 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30495 838 5.1 %RANDOM
Rwork0.26322 ---
obs0.26535 15674 90.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.895 Å2
Baniso -1Baniso -2Baniso -3
1-2.44 Å20 Å21.36 Å2
2---0.89 Å2-0 Å2
3----1.82 Å2
Refinement stepCycle: 1 / Resolution: 2.7→57.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3843 0 58 0 3901
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193990
X-RAY DIFFRACTIONr_bond_other_d0.0020.023690
X-RAY DIFFRACTIONr_angle_refined_deg1.6931.9635440
X-RAY DIFFRACTIONr_angle_other_deg1.062.9818525
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3465499
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.96425.166151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.04415638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7141514
X-RAY DIFFRACTIONr_chiral_restr0.0930.2634
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214392
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02732
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_it0.8171.7682026
X-RAY DIFFRACTIONr_mcbond_other0.8171.7682025
X-RAY DIFFRACTIONr_mcangle_it1.4952.6472515
X-RAY DIFFRACTIONr_mcangle_other1.4952.6482516
X-RAY DIFFRACTIONr_scbond_it0.8582.051964
X-RAY DIFFRACTIONr_scbond_other0.8592.0541965
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5353.0552926
X-RAY DIFFRACTIONr_long_range_B_refined3.86922.4944387
X-RAY DIFFRACTIONr_long_range_B_other3.86922.5234388
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 14820 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 43 -
Rwork0.409 1153 -
obs--89.59 %
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)
17.2907-0.69881.13826.4747-1.95450.82120.0523-0.0561-0.5269-0.1832-0.4305-1.70.04890.35690.37820.76690.06730.21260.5510.04090.601214.0939.51853.047
22.0970.8059-0.96152.8066-1.60793.5116-0.03280.36450.2332-0.24380.11520.0165-0.0336-0.1558-0.08240.46620.00870.23290.06390.04760.1491-5.26511.07439.575
32.57054.26361.44168.96750.05097.23960.4972-0.5835-0.31661.5981-0.6601-0.9777-0.41450.62120.16290.71560.09960.02440.7246-0.08050.446734.49238.02820.018
42.04271.1124-1.02943.4038-1.62623.5407-0.11150.0069-0.0522-0.0860.23460.20980.2575-0.4365-0.12310.4355-0.03420.22710.11250.02430.151213.85335.8768.865
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 112
2X-RAY DIFFRACTION2A113 - 317
3X-RAY DIFFRACTION3B1 - 112
4X-RAY DIFFRACTION4B113 - 317

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