+Open data
-Basic information
Entry | Database: PDB / ID: 7mmm | |||||||||
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Title | LyeTx I | |||||||||
Components | Toxin LyeTx 1 | |||||||||
Keywords | ANTIMICROBIAL PROTEIN / Lycosa erythrognatha / Antimicrobial peptide / LyeTx / Spider venom. | |||||||||
Function / homology | hemolysis in another organism / toxin activity / defense response to bacterium / extracellular region / Toxin LyeTx 1 Function and homology information | |||||||||
Biological species | Lycosa erythrognatha (spider) | |||||||||
Method | SOLUTION NMR / simulated annealing | |||||||||
Authors | Verly, R.M. | |||||||||
Funding support | Brazil, 2items
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Citation | Journal: Amino Acids / Year: 2010 Title: LyeTx I, a potent antimicrobial peptide from the venom of the spider Lycosa erythrognatha Authors: Verly, R.M. / Lima, M.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mmm.cif.gz | 168 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mmm.ent.gz | 145 KB | Display | PDB format |
PDBx/mmJSON format | 7mmm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mmm_validation.pdf.gz | 353.3 KB | Display | wwPDB validaton report |
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Full document | 7mmm_full_validation.pdf.gz | 478.6 KB | Display | |
Data in XML | 7mmm_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 7mmm_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mm/7mmm ftp://data.pdbj.org/pub/pdb/validation_reports/mm/7mmm | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 2837.517 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Lycosa erythrognatha (spider) / References: UniProt: C0HJU9 |
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Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution / Contents: 2 mM LyeTx I, 95% H2O/5% D2O / Label: LyeTx I - DPC / Solvent system: 95% H2O/5% D2O |
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Sample | Conc.: 2 mM / Component: LyeTx I / Isotopic labeling: natural abundance |
Sample conditions | Ionic strength: 20 mM / Label: LyeTx I - DPC / pH: 7 / Pressure: 1 atm / Temperature: 293 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE DRX / Manufacturer: Bruker / Model: AVANCE DRX / Field strength: 600 MHz Details: triple-resonance (1H/13C/15N) gradient probe (5 mm diameter)] |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | |||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | |||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 |