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- PDB-2kgt: Solution structure of SH3 domain of PTK6 -

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Basic information

Entry
Database: PDB / ID: 2kgt
TitleSolution structure of SH3 domain of PTK6
ComponentsTyrosine-protein kinase 6
KeywordsTRANSFERASE / SH3 domain / Src kinase / PTK6 / ATP-binding / Cytoplasm / Kinase / Nucleotide-binding / Nucleus / Phosphoprotein / Polymorphism / SH2 domain / Tyrosine-protein kinase
Function / homology
Function and homology information


negative regulation of protein tyrosine kinase activity / PTK6 Activates STAT3 / PTK6 Regulates Proteins Involved in RNA Processing / intestinal epithelial cell differentiation / PTK6 Regulates Cell Cycle / PTK6 promotes HIF1A stabilization / ERBB2 signaling pathway / negative regulation of growth / ERBB2 Activates PTK6 Signaling / PTK6 Expression ...negative regulation of protein tyrosine kinase activity / PTK6 Activates STAT3 / PTK6 Regulates Proteins Involved in RNA Processing / intestinal epithelial cell differentiation / PTK6 Regulates Cell Cycle / PTK6 promotes HIF1A stabilization / ERBB2 signaling pathway / negative regulation of growth / ERBB2 Activates PTK6 Signaling / PTK6 Expression / tyrosine phosphorylation of STAT protein / positive regulation of epidermal growth factor receptor signaling pathway / PTK6 Down-Regulation / positive regulation of DNA replication / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of cell cycle / cellular response to retinoic acid / positive regulation of tyrosine phosphorylation of STAT protein / cell surface receptor protein tyrosine kinase signaling pathway / ruffle / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / SCF(Skp2)-mediated degradation of p27/p21 / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Cyclin D associated events in G1 / Cytoprotection by HMOX1 / positive regulation of neuron projection development / 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 / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH3 type barrels. / SH2 domain / Src homology 3 domains ...PTK6, SH2 domain / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH3 type barrels. / 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 / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Protein-tyrosine kinase 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsLee, W. / Ko, S.
CitationJournal: To be Published
Title: The solution structure of SH3 domain of PTK6
Authors: Lee, W. / Ko, S.
History
DepositionMar 18, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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)8,3341
Polymers8,3341
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1lowest energy

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Components

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


Mass: 8334.204 Da / Num. of mol.: 1 / Fragment: SH3 domain, residues 1-72
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, receptor protein-tyrosine kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D HN(CA)CB
1223D HNCA
1323D HNCO
1423D CBCA(CO)NH
1523D HBHA(CO)NH
1623D (H)CCH-TOCSY
1713D 1H-15N NOESY
1823D 1H-13C NOESY
1912D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.2mM [U-99% 15N] SH domain-1, 90% H2O/10% D2O90% H2O/10% D2O
20.2mM [U-99% 13C; U-99% 15N] SH domain-2, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMSH domain-1[U-99% 15N]1
0.2 mMSH domain-2[U-99% 13C; U-99% 15N]2
Sample conditionsIonic strength: 100 / pH: 7 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Varian INOVAVarianINOVA9002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.2.5Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.2.5Guntert, Mumenthaler and Wuthrichrefinement
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
MOLMOLKoradi, Billeter and Wuthrichstructure analysis
PyMOLDeLano Scientific LLC.structure analysis
PyMOLDeLano Scientific LLC.peak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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