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Open data
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Basic information
Entry | Database: PDB / ID: 5gvo | ||||||
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Title | Solution NMR structure of a new lasso peptide sphaericin | ||||||
![]() | Uncharacterized protein | ||||||
![]() | UNKNOWN FUNCTION / lasso peptide / antibacterial / Structure from MOLMOL | ||||||
Function / homology | Putative lasso peptide![]() | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
![]() | Hemmi, H. / Kodani, S. / Inoue, Y. / Suzuki, M. / Dohra, H. / Suzuki, T. / Ohnishi-Kameyama, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Sphaericin, a Lasso Peptide from the Rare Actinomycete Planomonospora sphaerica Authors: Kodani, S. / Inoue, Y. / Suzuki, M. / Dohra, H. / Suzuki, T. / Hemmi, H. / Ohnishi-Kameyama, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77.3 KB | Display | ![]() |
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PDB format | ![]() | 61.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 378.4 KB | Display | ![]() |
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Full document | ![]() | 458.5 KB | Display | |
Data in XML | ![]() | 7.5 KB | Display | |
Data in CIF | ![]() | 10.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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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: 2175.509 Da / Num. of mol.: 1 / Fragment: UNP residues 22-39 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Type: solution / Contents: 10 mg/mL NA-C,H peptide, DMSO / Label: sample / Solvent system: DMSO |
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Sample | Conc.: 10 mg/mL / Component: peptide / Isotopic labeling: NA-C,H |
Sample conditions | Ionic strength: not detected Not defined / Label: condition / PH units: Not defined / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 2 | |||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 300 / Conformers submitted total number: 15 |