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Yorodumi- PDB-2kup: Solution structure of the complex of the PTB domain of SNT-2 and ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kup | ||||||
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Title | Solution structure of the complex of the PTB domain of SNT-2 and 19-residue peptide (aa 1571-1589) of HALK | ||||||
Components |
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Keywords | SIGNALING PROTEIN/ONCOPROTEIN / Complex / SNT-2 / PTB DOMAIN / hALK / structural genomics / signaling protein / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI / SIGNALING PROTEIN-ONCOPROTEIN complex | ||||||
Function / homology | Function and homology information ASP-3026-resistant ALK mutants / NVP-TAE684-resistant ALK mutants / alectinib-resistant ALK mutants / brigatinib-resistant ALK mutants / ceritinib-resistant ALK mutants / crizotinib-resistant ALK mutants / lorlatinib-resistant ALK mutants / MDK and PTN in ALK signaling / receptor signaling protein tyrosine kinase activator activity / regulation of dopamine receptor signaling pathway ...ASP-3026-resistant ALK mutants / NVP-TAE684-resistant ALK mutants / alectinib-resistant ALK mutants / brigatinib-resistant ALK mutants / ceritinib-resistant ALK mutants / crizotinib-resistant ALK mutants / lorlatinib-resistant ALK mutants / MDK and PTN in ALK signaling / receptor signaling protein tyrosine kinase activator activity / regulation of dopamine receptor signaling pathway / response to environmental enrichment / fibroblast growth factor receptor binding / ALK mutants bind TKIs / swimming behavior / transmembrane receptor protein tyrosine kinase adaptor activity / positive regulation of dendrite development / RND1 GTPase cycle / RND2 GTPase cycle / regulation of neuron differentiation / adult behavior / Signaling by ALK / neuron development / fibroblast growth factor receptor signaling pathway / Activated NTRK2 signals through FRS2 and FRS3 / negative regulation of lipid catabolic process / energy homeostasis / peptidyl-tyrosine autophosphorylation / FRS-mediated FGFR3 signaling / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / FRS-mediated FGFR1 signaling / cell surface receptor protein tyrosine kinase signaling pathway / transmembrane receptor protein tyrosine kinase activity / hippocampus development / receptor protein-tyrosine kinase / Signaling by ALK fusions and activated point mutants / positive regulation of NF-kappaB transcription factor activity / heparin binding / regulation of cell population proliferation / RAF/MAP kinase cascade / regulation of apoptotic process / protein tyrosine kinase activity / protein autophosphorylation / receptor complex / phosphorylation / signal transduction / protein-containing complex / extracellular exosome / ATP binding / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / distance geometry | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Li, H. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Struct.Funct.Genom. / Year: 2010 Title: Structural basis for the recognition of nucleophosmin-anaplastic lymphoma kinase oncoprotein by the phosphotyrosine binding domain of Suc1-associated neurotrophic factor-induced tyrosine-phosphorylated target-2 Authors: Koshiba, S. / Li, H. / Motoda, Y. / Tomizawa, T. / Kasai, T. / Tochio, N. / Yabuki, T. / Harada, T. / Watanabe, S. / Tanaka, A. / Shirouzu, M. / Kigawa, T. / Yamamoto, T. / Yokoyama, S. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kup.cif.gz | 996.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kup.ent.gz | 839.1 KB | Display | PDB format |
PDBx/mmJSON format | 2kup.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2kup_validation.pdf.gz | 364.8 KB | Display | wwPDB validaton report |
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Full document | 2kup_full_validation.pdf.gz | 575.8 KB | Display | |
Data in XML | 2kup_validation.xml.gz | 58.9 KB | Display | |
Data in CIF | 2kup_validation.cif.gz | 78.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/2kup ftp://data.pdbj.org/pub/pdb/validation_reports/ku/2kup | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 16332.278 Da / Num. of mol.: 1 / Fragment: PTB domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: cell-free synthesis (others) / References: UniProt: O43559 |
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#2: Protein/peptide | Mass: 2343.644 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized / References: UniProt: Q9UM73 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.37mM [U-13C; U-15N] (SNT-2 PTB domain)-1, 0.37mM (hALK peptide)-2, 20mM [U-2H] TRIS-3, 100mM sodium chloride-4, 1mM [U-2H] DTT-5, 0.02% sodium azide-6, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 120 / pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: distance geometry / Software ordinal: 1 | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 20 / Conformers submitted total number: 20 / Representative conformer: 1 |