BMRB Entry 34406

Title:
Solution NMR structure of the peptide 12530 from medicinal leech Hirudo medicinalis in dodecylphosphocholine micelles
Deposition date:
2019-05-21
Original release date:
2019-10-22
Authors:
Talyzina, I.; Nadezhdin, K.; Grafskaia, E.; Arseniev, A.; Lazarev, V.
Citation:

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).
PubMed: 31302447

Assembly members:

Assembly members:
entity_1, polymer, 11 residues, 1427.816 Da.

Natural source:

Natural source:   Common Name: medicinal leech   Taxonomy ID: 6421   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Hirudo medicinalis

Experimental source:

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: KFKKVIWKSFL

Data sets:
Data typeCount
13C chemical shifts50
15N chemical shifts11
1H chemical shifts111

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11

Entities:

Entity 1, entity_1 11 residues - 1427.816 Da.

1   LYSPHELYSLYSVALILETRPLYSSERPHE
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:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_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 peaks
SPARKY: Backbone or all simulated peaks