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Open data
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Basic information
Entry | Database: PDB / ID: 1xkm | ||||||
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Title | NMR structure of antimicrobial peptide distinctin in water | ||||||
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![]() | ANTIBIOTIC / PORE-FORMING PEPTIDE / HETERODIMER / HOMODIMER / DISULFIDE / FOUR-HELIX BUNDLE | ||||||
Method | SOLUTION NMR / simulated annealing with cartesian coordinate dynamics | ||||||
![]() | Amodeo, P. / Raimondo, D. / Andreotti, G. / Motta, A. / Scaloni, A. | ||||||
![]() | ![]() Title: A folding-dependent mechanism of antimicrobial peptide resistance to degradation unveiled by solution structure of distinctin. Authors: Raimondo, D. / Andreotti, G. / Saint, N. / Amodeo, P. / Renzone, G. / Sanseverino, M. / Zocchi, I. / Molle, G. / Motta, A. / Scaloni, A. #1: Journal: Febs Lett. / Year: 2001 Title: A novel heterodimeric antimicrobial peptide from the tree-frog Phyllomedusa distincta Authors: Batista, C.V. / Scaloni, A. / Rigden, D.J. / Silva, L.R. / Rodrigues Romero, A. / Dukor, R. / Sebben, A. / Talamo, F. / Bloch, C. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 751.1 KB | Display | ![]() |
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PDB format | ![]() | 653.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 375.9 KB | Display | ![]() |
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Full document | ![]() | 834.8 KB | Display | |
Data in XML | ![]() | 30.4 KB | Display | |
Data in CIF | ![]() | 55.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar 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: 2532.076 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: The peptide was prepared by solid-phase synthesis. This sequence occurs naturally in the tree-frog Phyllomedusa distincta #2: Protein/peptide | Mass: 2960.563 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: The peptide was prepared by solid-phase synthesis. This sequence occurs naturally in the tree-frog Phyllomedusa distincta |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using standard 2D homonuclear techniques. |
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Sample preparation
Details |
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Sample conditions |
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-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz |
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Processing
NMR software |
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Refinement | Method: simulated annealing with cartesian coordinate dynamics Software ordinal: 1 Details: the structures are based on a total of 636 restraints, 548 are NOE-derived distance constraints, 88 distance restraints from hydrogen bonds. | ||||||||||||||||||||
NMR representative | Selection criteria: structure within a prefixed threshold of amber energy, solvent accessible surface area and symmetry-based penalty functions | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: Structures within a prefixed threshold of amber energy, solvent accessible surface area and symmetry-based penalty functions (see jrnl) Conformers calculated total number: 150 / Conformers submitted total number: 24 |