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Yorodumi- PDB-1tyk: SOLUTION STRUCTURE OF A TOXIN FROM THE TARANTULA, GRAMMOSTOLA SPA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tyk | |||||||||
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Title | SOLUTION STRUCTURE OF A TOXIN FROM THE TARANTULA, GRAMMOSTOLA SPATULATA, WHICH INHIBITS MECHANOSENSITIVE ION CHANNELS | |||||||||
Components | Toxin GsMTx-4 | |||||||||
Keywords | TOXIN / INHIBITOR / CYSTEINE KNOT / BETA-SHEET | |||||||||
Function / homology | Function and homology information ion channel inhibitor activity / sodium channel regulator activity / potassium channel regulator activity / toxin activity / defense response to bacterium / lipid binding / extracellular region Similarity search - Function | |||||||||
Biological species | Grammostola rosea (Chilean rose tarantula) | |||||||||
Method | SOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING, RAMACHANDRAN REFINEMENT | |||||||||
Authors | Oswald, R.E. / Suchyna, T.M. / Mcfeeters, R. / Gottlieb, P. / Sachs, F. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Solution Structure of Peptide Toxins that Block Mechanosensitive Ion Channels Authors: Oswald, R.E. / Suchyna, T.M. / Mcfeeters, R. / Gottlieb, P. / Sachs, F. #1: Journal: J.Gen.Physiol. / Year: 2000 Title: Identification of a Peptide Toxin from Grammostola Spatulata Spider Venom that Blocks Cation-Selective Stretch-Activated Channels Authors: Suchyna, T.M. / Johnson, J.H. / Hamer, K. / Leykam, J.F. / Gage, D.A. / Clemo, H.F. / Baumgarten, C.M. / Sachs, F. #2: Journal: Toxicon / Year: 2003 Title: cDNA sequence and in vitro folding of GsMTX4, a specific peptide inhibitor of mechanosensitive channels Authors: Ostrow, K.L. / Mammoser, A. / Suchyna, T. / Sachs, F. / Oswald, R. / Kubo, S. / Chino, N. / Gottlieb, P.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tyk.cif.gz | 217.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tyk.ent.gz | 187.7 KB | Display | PDB format |
PDBx/mmJSON format | 1tyk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ty/1tyk ftp://data.pdbj.org/pub/pdb/validation_reports/ty/1tyk | HTTPS FTP |
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-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/peptide | Mass: 4109.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: VENOM Source: (natural) Grammostola rosea (Chilean rose tarantula) References: UniProt: Q7YT39 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: H-D EXCHANGE USING 2D TOCSY FOLLOWING RESUSPENSION OF LYOPHILIZED PROTEIN IN 100% D2O |
-Sample preparation
Details | Contents: 2 MM NATURAL ABUNDANCE GSMTX4 / Solvent system: H2O |
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Sample conditions | Ionic strength: 1 mM NACL / pH: 4.5 / Pressure: AMBIENT / Temperature: 278 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: DISTANCE GEOMETRY, SIMULATED ANNEALING, RAMACHANDRAN REFINEMENT Software ordinal: 1 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS, STRUCTURES WITH THE LOWEST ENERGY Conformers calculated total number: 200 / Conformers submitted total number: 20 |