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- PDB-1vm3: Solution structure of a membrane-targeting peptide designed based... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1vm3 | ||||||
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Title | Solution structure of a membrane-targeting peptide designed based on the N-terminal sequence of E. coli enzyme IIA (Glucose) | ||||||
![]() | peptide A3 | ||||||
![]() | ANTIBIOTIC / amphipathic helix / antimicrobial peptide / bacterial membrane anchor / membrane binding | ||||||
Biological species | synthetic construct (others) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
![]() | Wang, G. / Li, X. | ||||||
![]() | ![]() Title: Correlation of Three-dimensional Structures with the Antibacterial Activity of a Group of Peptides Designed Based on a Nontoxic Bacterial Membrane Anchor. Authors: Wang, G. / Li, Y. / Li, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 26 KB | Display | ![]() |
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PDB format | ![]() | 17.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 336.7 KB | Display | ![]() |
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Full document | ![]() | 349.8 KB | Display | |
Data in XML | ![]() | 3.1 KB | Display | |
Data in CIF | ![]() | 3.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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: 1438.668 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The peptide was synthesized using the solid-phase method and purified by HPLC. 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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NMR details | Text: This structure was determined using standard 2D homonuclear NMR techniques, plus the use of backbone angle restraints derived from a set of heteronuclear chemical shifts measured on the natural ...Text: This structure was determined using standard 2D homonuclear NMR techniques, plus the use of backbone angle restraints derived from a set of heteronuclear chemical shifts measured on the natural abundance peptide bound to micelles. |
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Sample preparation
Details | Contents: 2mM peptide, 80mM sodium dodecylsulfate, 90% H2O and 10% D2O Solvent system: 90% H2O and 10% D2O |
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Sample conditions | pH: 5.4 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: The structures are based on 104 distances derived from the NOESY spectra, 20 backbone dihedral angles derived from a set of chemical shifts using the NMR program TALOS, and 5 chi1 angle restraints. | ||||||||||||||||||||
NMR representative | Selection criteria: most resemble the average structure | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: No NOE violations greater than 0.50 A, rms difference for bond deviations from ideality less than 0.01 A, rms difference for angle deviations from ideality less than 5 ...Conformer selection criteria: No NOE violations greater than 0.50 A, rms difference for bond deviations from ideality less than 0.01 A, rms difference for angle deviations from ideality less than 5 degrees, Structures with the lowerest energies in the ensemble. Conformers calculated total number: 100 / Conformers submitted total number: 5 |