+Open data
-Basic information
Entry | Database: PDB / ID: 2lde | ||||||
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Title | Solution structure of the long sarafotoxin srtx-i3 | ||||||
Components | Sarafotoxin-i3 | ||||||
Keywords | TOXIN / endothelin-like peptide | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Cordier, F. / Zorba, A. / Hajj, M. / Ducancel, F. / Servent, D. / Delepierre, M. | ||||||
Citation | Journal: Biochimie / Year: 2012 Title: Pharmacological and structural characterization of long-sarafotoxins, a new family of endothelin-like peptides: Role of the C-terminus extension. Authors: Mourier, G. / Hajj, M. / Cordier, F. / Zorba, A. / Gao, X. / Coskun, T. / Herbet, A. / Marcon, E. / Beau, F. / Delepierre, M. / Ducancel, F. / Servent, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2lde.cif.gz | 86.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2lde.ent.gz | 51.2 KB | Display | PDB format |
PDBx/mmJSON format | 2lde.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ld/2lde ftp://data.pdbj.org/pub/pdb/validation_reports/ld/2lde | 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: 2967.405 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 3 mM srtx-i3, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O | |||||||||||||||
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Sample | Conc.: 3 mM / Component: srtx-i3-1 | |||||||||||||||
Sample conditions |
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-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 Details: Of the 200 calculated conformers, the 80 conformers with the lowest total energy were refined in water. The 10 refined conformers of lowest energy represent the final ensemble. | ||||||||||||||||||||||||
NMR constraints | NOE constraints total: 445 / NOE intraresidue total count: 183 / NOE long range total count: 20 / NOE medium range total count: 101 / NOE sequential total count: 141 / Hydrogen bond constraints total count: 6 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0.456 Å | ||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.032 Å / Distance rms dev error: 0.005 Å |