BMRB Entry 34406

Name: Solution NMR structure of the peptide 12530 from medicinal leech Hirudo medicinalis in dodecylphosphocholine micelles
Published: 2019-10-22

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PDB ID: 6rsm
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34406
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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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:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
13C chemical shifts	50
15N chemical shifts	11
1H chemical shifts	111

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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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

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 peaks
SPARKY: Backbone or all simulated peaks