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- PDB-6vy7: Structural characterization of novel conotoxin MIIIB derived from... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6vy7 | |||||||||
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Title | Structural characterization of novel conotoxin MIIIB derived from Conus magus | |||||||||
![]() | Conotoxin MIIIB | |||||||||
![]() | TOXIN / venom peptide | |||||||||
Function / homology | Conotoxin / Conotoxin / ion channel inhibitor activity / : / extracellular region / Conotoxin superfamily M![]() | |||||||||
Biological species | ![]() | |||||||||
Method | SOLUTION NMR / simulated annealing | |||||||||
![]() | Loening, N.M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Discovery and characterization of novel conotoxin MIIIB derived from Conus magus: The expansion of conotoxin diversity Authors: Zhang, R.-Y. / Espirtu, M.J. / Loening, N.M. / Kapono, C.A. / Bingham, J.-P. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 109 KB | Display | ![]() |
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PDB format | ![]() | 74.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 500.3 KB | Display | ![]() |
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Full document | ![]() | 674.3 KB | Display | |
Data in XML | ![]() | 28.5 KB | Display | |
Data in CIF | ![]() | 29.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein/peptide | Mass: 2457.898 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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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 MIIIB Isomer F, 0.5 mM DSS, 95% H2O/5% D2O Details: Synthetically produced MIIIB purified by prep RP-HPLC and analytical RP-HPLC to isolate isomer F, which has the disulfide connectivity C1-C6, C2-C4, C3-C5. Label: MIIIB_Isomer_F / Solvent system: 95% H2O/5% D2O | ||||||||||||
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Sample |
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Sample conditions | Details: Sample prepared by dissolving lyophilized peptide in 95% H2O/5% D2O with 0.5 mM DSS, pH was adjusted to 3.8 using dropwise addition of 500 mM hydrochloric acid. Ionic strength: 0 mM / Label: conditions_1 / pH: 3.8 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 800 MHz / Details: TCI cryoprobe |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: log harmonic potential used, water refinement used for 20 lowest energy structure | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |