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- PDB-6mi9: The peptide PaAMP1B3 is an analog derived from the PaAMP1. The se... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6mi9 | ||||||
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Title | The peptide PaAMP1B3 is an analog derived from the PaAMP1. The sequence of the ribosomal protein of Pyrobaculum aerophylum was used as template for rational design, using the Joker algorithm. | ||||||
![]() | PRO-MET-ALA-ARG-ASN-LYS-ILE-LEU-GLY-LYS-ILE-LEU-ARG-LYS-ILE-ALA-ALA-PHE-LYS | ||||||
![]() | ANTIMICROBIAL PROTEIN / PAM | ||||||
Biological species | synthetic construct (others) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
![]() | Mundim, H.M. / Alves, E.S.F. / Rodrigues, L.V. / Liao, L.M. | ||||||
![]() | ![]() Title: NMR SOLUTION STRUCTURE OF THE ANTIMICROBIAL PEPTIDE PAAMP1B3. Authors: Mundim, H.M. / Alves, E.S.F. / Liao, L.M. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 61.7 KB | Display | ![]() |
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PDB format | ![]() | 48.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 241.4 KB | Display | ![]() |
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Full document | ![]() | 295.2 KB | Display | |
Data in XML | ![]() | 6.1 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: 2172.791 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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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: 1 mM PaAMP1B3, 100 mM [U-98% 2H] SDS-D25, 5 % v/v [U-98% 2H] TMSP-d4, 90 % v/v H2O, 10 % v/v [U-99% 2H] D2O, 90% H2O/10% D2O Label: PaAMP1B3 / Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: acid Not defined / Label: PaAMP1B3 / pH: 4.3 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 500 MHz |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 4 | ||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 10 |