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- PDB-2jx6: Structure and membrane interactions of the antibiotic peptide der... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2jx6 | ||||||
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Title | Structure and membrane interactions of the antibiotic peptide dermadistinctin k by solution and oriented 15N and 31P solid-state NMR spectroscopy | ||||||
![]() | Dermadistinctin-K | ||||||
![]() | ANTIMICROBIAL PROTEIN / ALPHA HELIX / AMPHIPATHIC CHARACTER / C-TERMINAL CARBOXYAMIDATION / MEMBRANE PEPTIDE / Amphibian defense peptide / Antibiotic / Antimicrobial / Secreted | ||||||
Function / homology | Dermaseptin / Dermaseptin / defense response to bacterium / extracellular region / Dermaseptin-DI1![]() | ||||||
Biological species | Phyllomedusa distincta (Sao Paulo leaf frog) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
![]() | Mendonca Moraes, C. / Verly, R.M. / Resende, J.M. / Bemquerer, M.P. / Pilo-Veloso, D. / Valente, A. / Almeida, F.C.L. / Bechinger, B. | ||||||
![]() | ![]() Title: Structure and membrane interactions of the antibiotic peptide dermadistinctin K by multidimensional solution and oriented 15N and 31P solid-state NMR spectroscopy Authors: Verly, R.M. / de Moraes, C.M. / Resende, J.M. / Aisenbrey, C. / Bemquerer, M.P. / Pilo-Veloso, D. / Valente, A.P. / Almeida, F.C.L. / Bechinger, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 181.1 KB | Display | ![]() |
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PDB format | ![]() | 158.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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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: 3156.699 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The peptide was synthesized by solid-phase synthesis using fmoc chemistry. The peptide is an antimicrobial peptide that is naturally found from the skin secretion of phyllomedusa distincta, ...Details: The peptide was synthesized by solid-phase synthesis using fmoc chemistry. The peptide is an antimicrobial peptide that is naturally found from the skin secretion of phyllomedusa distincta, a frog species found in brazilian forests. Source: (synth.) Phyllomedusa distincta (Sao Paulo leaf frog) References: UniProt: P83638 |
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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: 2.0mM dermadistinctin k; trifluoroethanol; H2O 60%, D2O 40% Solvent system: trifluoroethanol; H2O 60%, D2O 40% |
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Sample | Conc.: 2.0 mM / Component: dermadistinctin k |
Sample conditions | pH: 7 / Pressure: ambient / Temperature: 293.15 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance DRX / Manufacturer: Bruker / Model: AVANCE DRX / Field strength: 600 MHz |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: NOE intensities were converted into semi-quantitative distances restrains. The upper limits of the distances thus obtained were 2.8, 3.4 and 5.0A; (for strong, medium, and weak NOEs, ...Details: NOE intensities were converted into semi-quantitative distances restrains. The upper limits of the distances thus obtained were 2.8, 3.4 and 5.0A; (for strong, medium, and weak NOEs, respectively). Structure calculations were performed using the Xplor-NIH software, version 2.17.0 . Starting with the extended structure, 500 structures were generated using a simulated annealing protocol. This was followed by 20000 steps of simulated annealing at 1000 K and a subsequent decrease in tempera ure in 15000 steps in the first slow-cool annealing stage. | ||||||||||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 294 / NOE intraresidue total count: 178 / NOE long range total count: 0 / NOE medium range total count: 38 / NOE sequential total count: 78 | ||||||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 500 / Conformers submitted total number: 20 / Representative conformer: 19 |