BMRB Entry 34705

Name: Hm-AMP2
Published: 2022-11-28

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PDB ID: 7qzv
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34705
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:

Hm-AMP2

Deposition date:

2022-02-01

Original release date:

2022-11-28

Authors:

Grafskaia, E.; Pavlova, E.; Latsis, I.; Malakhova, M.; Lavrenova, V.; Ivchenkov, D.; Bashkirov, P.; Kot, E.; Mineev, K.; Arseniev, A.; Klinov, D.; Lazarev, V.

Citation:

Citation: Grafskaia, E.; Pavlova, E.; Latsis, I.; Malakhova, M.; Ivchenkov, D.; Bashkirov, P.; Kot, E.; Mineev, K.; Arseniev, A.; Klinov, D.; Lazarev, V.. "Non-toxic antimicrobial peptide Hm-AMP2 from leech metagenome proteins identified by the gradient-boosting approach" Materials 224, 111364-. (2022).

Assembly members:

Assembly members:
entity_1, polymer, 13 residues, 1730.047 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: EKRWRRLIFNYFX

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
13C chemical shifts	40
15N chemical shifts	15
1H chemical shifts	107

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 13 residues - 1730.047 Da.

1

GLU

LYS

ARG

TRP

ARG

LEU

ILE

PHE

ASN

2

TYR

PHE

NH2

Samples:

sample_1: prok_2590_2 peptide 0.85 mM; dodecyl phosphocholine, [U-2H], 85 mM; sodium acetate, [U-2H], 20 mM; sodium azide 0.01 % w/w; D2O, [U-2H], 5 % v/v

sample_conditions_1: ionic strength: 20 mM; pH: 4.8; pressure: 1 atm; temperature: 303.0 K

Experiments:

Name	Sample	Sample state	Sample conditions
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-TOCSY	sample_1	isotropic	sample_conditions_1

Software:

TopSpin v3.2, Bruker Biospin - collection

CARA v1.9.1.7, Keller and Wuthrich - chemical shift assignment, peak picking

CYANA v3.98.5, Guntert, Mumenthaler and Wuthrich - structure calculation

NMR spectrometers:

Bruker AVANCE II 700 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks