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- PDB-8s1c: Intertwined dimer of the PTK6 SH3 domain -

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Basic information

Entry
Database: PDB / ID: 8s1c
TitleIntertwined dimer of the PTK6 SH3 domain
ComponentsProtein-tyrosine kinase 6
KeywordsCYTOSOLIC PROTEIN / kinase / SH3 domain / PTK6 / BRK / Non-receptor tyrosine-protein kinase
Function / homology
Function and homology information


PTK6 Activates STAT3 / negative regulation of protein tyrosine kinase activity / PTK6 Regulates Proteins Involved in RNA Processing / intestinal epithelial cell differentiation / tyrosine phosphorylation of STAT protein / ERBB2 signaling pathway / negative regulation of growth / PTK6 Expression / positive regulation of epidermal growth factor receptor signaling pathway / PTK6 Down-Regulation ...PTK6 Activates STAT3 / negative regulation of protein tyrosine kinase activity / PTK6 Regulates Proteins Involved in RNA Processing / intestinal epithelial cell differentiation / tyrosine phosphorylation of STAT protein / ERBB2 signaling pathway / negative regulation of growth / PTK6 Expression / positive regulation of epidermal growth factor receptor signaling pathway / PTK6 Down-Regulation / PTK6 promotes HIF1A stabilization / ERBB2 Activates PTK6 Signaling / PTK6 Regulates Cell Cycle / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / cellular response to retinoic acid / positive regulation of cell cycle / ruffle / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / positive regulation of DNA replication / positive regulation of receptor signaling pathway via JAK-STAT / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / Cytoprotection by HMOX1 / positive regulation of neuron projection development / SCF(Skp2)-mediated degradation of p27/p21 / cell surface receptor protein tyrosine kinase signaling pathway / Cyclin D associated events in G1 / cell migration / protein tyrosine kinase activity / protein autophosphorylation / histone H3Y41 kinase activity / histone H2AXY142 kinase activity / cell differentiation / nuclear body / protein phosphorylation / signaling receptor binding / innate immune response / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
PTK6, SH2 domain / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily ...PTK6, SH2 domain / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Protein-tyrosine kinase 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsOeguetcue, D. / Berndt, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)421152132 Germany
CitationJournal: To Be Published
Title: Intertwined dimer of the PTK6 SH3 domain
Authors: Oeguetcue, D. / Berndt, S.
History
DepositionFeb 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein-tyrosine kinase 6
B: Protein-tyrosine kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,29618
Polymers16,8792
Non-polymers41816
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-182 kcal/mol
Surface area7420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.170, 42.750, 94.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Protein-tyrosine kinase 6 / Breast tumor kinase / Tyrosine-protein kinase BRK


Mass: 8439.304 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTK6, BRK / Production host: Escherichia coli (E. coli)
References: UniProt: Q13882, non-specific protein-tyrosine kinase
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.53 Å3/Da / Density % sol: 51.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 2.5 M Sodium chloride 100 mM Sodium Potassium phosphate; pH 6.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Sep 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.75→38.53 Å / Num. obs: 16795 / % possible obs: 84.5 % / Redundancy: 13.7 % / Biso Wilson estimate: 23.72 Å2 / CC1/2: 0.88 / CC star: 0.904 / Net I/av σ(I): 0.71 / Net I/σ(I): 18.8
Reflection shellResolution: 1.75→1.813 Å / Num. unique obs: 16788 / CC1/2: 0.92 / % possible all: 82.01

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
PDB_EXTRACTdata extraction
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→38.53 Å / SU ML: 0.2116 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 24.5281
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2226 842 5.02 %
Rwork0.194 15946 -
obs0.1954 16788 93.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.92 Å2
Refinement stepCycle: LAST / Resolution: 1.75→38.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms970 0 16 136 1122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00871004
X-RAY DIFFRACTIONf_angle_d0.93031368
X-RAY DIFFRACTIONf_chiral_restr0.057135
X-RAY DIFFRACTIONf_plane_restr0.011173
X-RAY DIFFRACTIONf_dihedral_angle_d13.2196330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.860.34881230.24022322X-RAY DIFFRACTION82.94
1.86-20.24091260.20352489X-RAY DIFFRACTION88.79
2-2.20.21681420.17742627X-RAY DIFFRACTION94.18
2.2-2.520.21071450.18692720X-RAY DIFFRACTION96.63
2.52-3.180.24391490.21762808X-RAY DIFFRACTION98.37
3.18-38.530.20321570.18222980X-RAY DIFFRACTION99.46

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