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- PDB-6eim: Human STK10 bound to GW683134A -

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Basic information

Entry
Database: PDB / ID: 6eim
TitleHuman STK10 bound to GW683134A
ComponentsSerine/threonine-protein kinase 10
KeywordsTRANSFERASE / kinase / inhibitor / complex / 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 / 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-B6E / Serine/threonine-protein kinase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.43 Å
AuthorsSorrell, F.J. / Berger, B.-T. / Salah, E. / von Delft, F. / Bountra, C. / Arrowsmith, C. / Edwards, A.M. / Knapp, S. / Elkins, J.M.
CitationJournal: To Be Published
Title: Human STK10 bound to GW683134
Authors: Sorrell, F.J. / Elkins, J.M.
History
DepositionSep 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)69,6389
Polymers68,2492
Non-polymers1,3897
Water13,367742
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-17 kcal/mol
Surface area26040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.468, 99.812, 125.839
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 34124.301 Da / Num. of mol.: 2
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-B6E / ~{N}-[5-[4-[[2-fluoranyl-5-(trifluoromethyl)phenyl]carbamoylamino]phenoxy]-1~{H}-benzimidazol-2-yl]furan-2-carboxamide


Mass: 539.438 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H17F4N5O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 742 / 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: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 10% PEG1000, 10% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.43→46.39 Å / Num. obs: 110558 / % possible obs: 96 % / Redundancy: 4.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.028 / Rrim(I) all: 0.061 / Net I/σ(I): 12.6 / Num. measured all: 449512 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.43-1.483.90.839106160.5350.450.95894.8
5.54-46.3940.03418860.9980.0180.03987.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.43 Å41.81 Å
Translation1.43 Å41.81 Å

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Processing

Software
NameVersionClassification
Aimless0.5.29data scaling
PHASER2.6.1phasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2j7t

2j7t


Resolution: 1.43→41.806 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.25
RfactorNum. reflection% reflection
Rfree0.1736 5487 4.97 %
Rwork0.1544 --
obs0.1554 110494 95.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.82 Å2 / Biso mean: 25.867 Å2 / Biso min: 9.22 Å2
Refinement stepCycle: final / Resolution: 1.43→41.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4469 0 162 742 5373
Biso mean--25.47 34.98 -
Num. residues----581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044847
X-RAY DIFFRACTIONf_angle_d0.6766621
X-RAY DIFFRACTIONf_chiral_restr0.063754
X-RAY DIFFRACTIONf_plane_restr0.005926
X-RAY DIFFRACTIONf_dihedral_angle_d24.2671843
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.43-1.44630.33791810.28353465364695
1.4463-1.46330.31091780.26593417359594
1.4633-1.48110.2811790.24823357353694
1.4811-1.49990.27381590.22963292345189
1.4999-1.51960.24511840.2193417360196
1.5196-1.54040.26791830.20733511369496
1.5404-1.56240.20621850.20623465365096
1.5624-1.58580.26161710.19233508367996
1.5858-1.61050.23851940.19213488368297
1.6105-1.63690.23991590.17823525368496
1.6369-1.66520.19151940.17423521371597
1.6652-1.69550.22881750.16633503367896
1.6955-1.72810.20621750.16313536371198
1.7281-1.76330.18961590.15653314347390
1.7633-1.80170.18372250.15133476370196
1.8017-1.84360.17721970.14573499369697
1.8436-1.88970.18771960.1433577377398
1.8897-1.94080.17512030.14083537374098
1.9408-1.99790.16441780.1323565374397
1.9979-2.06240.15251710.12833589376097
2.0624-2.13610.16482030.1333588379198
2.1361-2.22160.16221740.13273539371396
2.2216-2.32270.15831760.12743459363594
2.3227-2.44520.14661820.13013594377698
2.4452-2.59830.17352020.13963593379597
2.5983-2.79890.16321950.14273571376697
2.7989-3.08050.15441900.15343600379096
3.0805-3.52610.15671720.15273409358191
3.5261-4.44170.1321680.14363582375094
4.4417-41.82350.18231790.17413510368989

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