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Yorodumi- PDB-7osc: Solution structure of antimicrobial peptide cathelicidin-1 PcDode... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7osc | ||||||
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Title | Solution structure of antimicrobial peptide cathelicidin-1 PcDode from sperm whale Physeter catodon | ||||||
Components | cathelicidin-1-like | ||||||
Keywords | ANTIMICROBIAL PROTEIN / CATHELICIDIN | ||||||
Function / homology | Cathelicidin, conserved site / Cathelicidins signature 2. / Cathelicidin-like / defense response / extracellular region / cathelicidin-1-like Function and homology information | ||||||
Biological species | Physeter macrocephalus (sperm whale) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Mironov, P.A. / Myshkin, M.Y. / Shenkarev, Z.O. | ||||||
Citation | Journal: Front Microbiol / Year: 2021 Title: Dodecapeptide Cathelicidins of Cetartiodactyla: Structure, Mechanism of Antimicrobial Action, and Synergistic Interaction With Other Cathelicidins Authors: Bolosov, I.A. / Panteleev, P.V. / Sychev, S.V. / Sukhanov, S.V. / Mironov, P.A. / Myshkin, M.Y. / Shenkarev, Z.O. / Ovchinnikova, T.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7osc.cif.gz | 160.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7osc.ent.gz | 136.3 KB | Display | PDB format |
PDBx/mmJSON format | 7osc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/os/7osc ftp://data.pdbj.org/pub/pdb/validation_reports/os/7osc | HTTPS FTP |
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-Related structure data
Related structure data | 7acbC 7aceC C: citing same article (ref.) |
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Similar structure data | |
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: 2787.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physeter macrocephalus (sperm whale) / Gene: LOC102973809 / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2Y9FJE4 |
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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: 0.6 mM PCdode, 5 % [U-100% 2H] D2O, 95% H2O/5% D2O Label: natural abundance / Solvent system: 95% H2O/5% D2O | ||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.01 mM / Label: condition_1 / pH: 4.4 / Pressure: 1 atm / Temperature: 313 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||
NMR representative | Selection criteria: target function | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 200 / Conformers submitted total number: 20 |