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- PDB-1rja: Solution Structure and Backbone Dynamics of the Nonreceptor Tyros... -

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Basic information

Entry
Database: PDB / ID: 1rja
TitleSolution Structure and Backbone Dynamics of the Nonreceptor Tyrosine Kinase PTK6/Brk SH2 Domain
ComponentsTyrosine-protein kinase 6
KeywordsTRANSFERASE / Human protein tyrosine kinase-6 (PTK6/Brk) / Src homology 2(SH2) domain / Solution structure / Backbone dynamics
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 / ERBB2 signaling pathway / negative regulation of growth / PTK6 Expression / tyrosine phosphorylation of STAT protein / positive regulation of epidermal growth factor receptor signaling pathway / PTK6 promotes HIF1A stabilization ...PTK6 Activates STAT3 / negative regulation of protein tyrosine kinase activity / PTK6 Regulates Proteins Involved in RNA Processing / intestinal epithelial cell differentiation / ERBB2 signaling pathway / negative regulation of growth / PTK6 Expression / tyrosine phosphorylation of STAT protein / positive regulation of epidermal growth factor receptor signaling pathway / PTK6 promotes HIF1A stabilization / ERBB2 Activates PTK6 Signaling / PTK6 Down-Regulation / PTK6 Regulates Cell Cycle / positive regulation of cell cycle / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / cellular response to retinoic acid / positive regulation of tyrosine phosphorylation of STAT protein / ruffle / cell surface receptor protein tyrosine kinase signaling pathway / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / positive regulation of DNA replication / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Cytoprotection by HMOX1 / SCF(Skp2)-mediated degradation of p27/p21 / positive regulation of neuron projection development / Cyclin D associated events in G1 / cell migration / protein tyrosine kinase activity / protein autophosphorylation / cell differentiation / nuclear body / protein phosphorylation / innate immune response / signaling receptor binding / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
PTK6, SH2 domain / SH2 domain / SHC Adaptor Protein / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily ...PTK6, SH2 domain / SH2 domain / SHC Adaptor Protein / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, 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 / Alpha Beta
Similarity search - Domain/homology
Protein-tyrosine kinase 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing
Model type detailsminimized average
AuthorsHong, E. / Shin, J. / Lee, W.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Solution Structure and Backbone Dynamics of the Non-receptor Protein-tyrosine Kinase-6 Src Homology 2 Domain
Authors: Hong, E. / Shin, J. / Kim, H.I. / Lee, S.T. / Lee, W.
#1: Journal: J.Biomol.NMR / Year: 2001
Title: Letter to the Editor: Complete sequence-specific 1H, 13C and 15N resonance assignments of the human PTK6 SH2 domain
Authors: Hong, E. / Shin, J. / Bang, E. / Kim, M.H. / Lee, S.T. / Lee, W.
History
DepositionNov 18, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 10, 2011Group: Source and taxonomy
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase 6


Theoretical massNumber of molelcules
Total (without water)11,3641
Polymers11,3641
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 50structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Tyrosine-protein kinase 6 / Breast tumor kinase / Tyrosine-protein kinase brk / PTK6/Brk


Mass: 11363.937 Da / Num. of mol.: 1 / Fragment: SH2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13882, EC: 2.7.1.112

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
1333D 13C-separated NOESY
1443D 13C-separated NOESY
NMR detailsText: This structure was determined using triple-resonance NMR

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM SH2 domain U-15N; 50mM phospahte buffer NA; 90% H2O, 10% D2O90% H2O/10% D2O
21mM SH2 domain U-15N, 13C; 50mM phospahte buffer NA; 90% H2O, 10% D2O90% H2O/10% D2O
31mM SH2 domain U-15N, 13C; 50mM phospahte buffer NA; 100% D2O100% D2O
41mM SH2 domain U-13C; 50mM phospahte buffer NA; 100% D2O100% D2O
Sample conditionsIonic strength: 0.15 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Bruker Gmb.data analysis
NMRPipe1.8Delaglio, F.processing
Sparky3.106Goddard, T.D.data analysis
CNS1refinement
Insight II98MSIstructure solution
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 21

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