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- PDB-4aot: Crystal Structure of Human Serine Threonine Kinase-10 (LOK) Bound... -

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Basic information

Entry
Database: PDB / ID: 4aot
TitleCrystal Structure of Human Serine Threonine Kinase-10 (LOK) Bound to GW830263A
ComponentsSerine/threonine-protein kinase 10
KeywordsTRANSFERASE / STK10 / LOK
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 / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity ...lymphocyte aggregation / regulation of lymphocyte migration / RHOB GTPase cycle / RHOC GTPase cycle / RHOA GTPase cycle / specific granule membrane / protein autophosphorylation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / intracellular signal transduction / nuclear body / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / Neutrophil degranulation / protein homodimerization activity / extracellular exosome / nucleoplasm / 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 / 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-GW8 / Serine/threonine-protein kinase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsElkins, J.M. / Salah, E. / Szklarz, M. / Canning, P. / von Delft, F. / Yue, W. / Liu, Y. / Bountra, C. / Arrowsmith, C. / Edwards, A. / Knapp, S.
CitationJournal: To be Published
Title: Crystal Structure of Human Serine Threonine Kinase-10 (Lok) Bound to Gw830263A
Authors: Elkins, J.M. / Salah, E. / Szklarz, M. / Canning, P. / von Delft, F. / Yue, W. / Liu, Y. / Bountra, C. / Arrowsmith, C. / Edwards, A. / Knapp, S.
History
DepositionMar 29, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: Derived calculations
Revision 1.2Dec 5, 2012Group: Database references / Structure summary
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Jun 13, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_seq_type / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / 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_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 / _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)70,06710
Polymers68,5972
Non-polymers1,4708
Water2,144119
1
A: Serine/threonine-protein kinase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0696
Polymers34,2991
Non-polymers7715
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine/threonine-protein kinase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9984
Polymers34,2991
Non-polymers7003
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.690, 87.510, 148.590
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:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 16 - 314 / Label seq-ID: 1 - 299

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

NCS oper: (Code: given
Matrix: (0.65808, -0.73001, 0.18445), (-0.7261, -0.55044, 0.41207), (-0.19928, -0.4051, -0.89229)
Vector: -13.88238, -4.57636, 15.35894)

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Components

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


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) / Gene: STK10, LOK / Plasmid: PNIC28-BSA4 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O94804, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GW8 / 1-(4-{methyl[2-({4-[(methylsulfonyl)methyl]phenyl}amino)pyrimidin-4-yl]amino}phenyl)-3-{3-[(4-methylpiperazin-1-yl)carbonyl]phenyl}urea / GW830263A


Mass: 628.744 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H36N8O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.64 Å3/Da / Density % sol: 53.4 % / Description: NONE
Crystal growpH: 6.5
Details: 0.2M NAI, 0.1M BISTRISPROPANE PH 6.5, 20% PEG3350, 10% ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173
DetectorType: ADSC CCD / Detector: CCD / 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: 2.33→56.64 Å / Num. obs: 31773 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 9.8
Reflection shellResolution: 2.33→2.42 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.19 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J7T

2j7t


Resolution: 2.33→75.4 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.908 / SU B: 14.08 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.315 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25221 1600 5 %RANDOM
Rwork0.21695 ---
obs0.21877 30113 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.835 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å20 Å20 Å2
2--1.52 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 2.33→75.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4291 0 96 119 4506
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.024491
X-RAY DIFFRACTIONr_bond_other_d0.0050.022971
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.9956109
X-RAY DIFFRACTIONr_angle_other_deg1.3353.0097277
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9375552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91624.358179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.26415739
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6391522
X-RAY DIFFRACTIONr_chiral_restr0.0840.2690
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214930
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02872
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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 NCS

Ens-ID: 1 / Number: 9023 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.33→2.391 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 106 -
Rwork0.293 1986 -
obs--99.76 %
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)
14.33670.46870.68011.1625-0.03251.15570.0360.5066-0.2796-0.1412-0.0405-0.1225-0.01590.11840.00440.02060.0190.01020.17730.0090.07575.268-20.89-6.997
22.12470.4863-0.00142.6832-0.35232.2371-0.07780.22840.473-0.0420.14080.4283-0.5295-0.2667-0.0630.16570.0968-0.00710.15350.09930.1983-2.4754.085-9.178
33.39570.57521.47111.74290.41712.7259-0.0253-0.16890.60660.14530.1605-0.2655-0.60880.5176-0.13520.4181-0.17050.06930.4205-0.12570.39227.0684.14616.3
42.31940.4319-0.01741.3480.40643.69590.0523-0.14710.24880.1596-0.07310.1565-0.2623-0.43350.02080.2399-0.01340.05920.2419-0.11750.15386.409-3.02127.784
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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