BMRB Entry 34406
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34406
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Title: Solution NMR structure of the peptide 12530 from medicinal leech Hirudo medicinalis in dodecylphosphocholine micelles PubMed: 31302447
Deposition date: 2019-05-21 Original release date: 2019-10-22
Authors: Talyzina, I.; Nadezhdin, K.; Grafskaia, E.; Arseniev, A.; Lazarev, V.
Citation: Grafskaia, E.; Nadezhdin, K.; Talyzina, I.; Polina, N.; Podgorny, O.; Pavlova, E.; Bashkirov, P.; Kharlampieva, D.; Bobrovsky, P.; Latsis, I.; Manuvera, V.; Babenko, V.; Trukhan, V.; Arseniev, A.; Klinov, D.; Lazarev, V.. "Medicinal leech antimicrobial peptides lacking toxicity represent a promising alternative strategy to combat antibiotic-resistant pathogens." Eur. J. Med. Chem. 180, 143-153 (2019).
Assembly members:
entity_1, polymer, 11 residues, 1427.816 Da.
Natural source: Common Name: medicinal leech Taxonomy ID: 6421 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Hirudo medicinalis
Experimental source: Production method: chemical synthesis
Entity Sequences (FASTA):
entity_1: KFKKVIWKSFL
- assigned_chemical_shifts
- spectral_peak_list
| Data type | Count |
| 13C chemical shifts | 50 |
| 15N chemical shifts | 11 |
| 1H chemical shifts | 111 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1 | 1 |
Entities:
Entity 1, entity_1 11 residues - 1427.816 Da.
| 1 | LYS | PHE | LYS | LYS | VAL | ILE | TRP | LYS | SER | PHE | ||||
| 2 | LEU |
Samples:
sample_1: peptide 12530 1 ± 0.2 mM; dodecylphosphocholine 100 ± 5 mM
sample_conditions_1: ionic strength: 0 M; pH: 4; pressure: 1 atm; temperature: 303 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aromatic | sample_1 | isotropic | sample_conditions_1 |
Software:
CYANA v3.98.5, Guntert, Mumenthaler and Wuthrich - structure calculation
CARA, Keller and Wuthrich - chemical shift assignment, peak picking
TopSpin, Bruker Biospin - collection, processing
TALOS, Cornilescu, Delaglio and Bax - data analysis
PSVS, Bhattacharya and Montelione - refinement
NMR spectrometers:
- Bruker Avance 800 MHz
- Bruker Avance 600 MHz
Download HSQC peak lists in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts