BMRB Entry 34706

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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/BMR34706
MolProbity Validation Chart

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Title:
Hm-AMP8
Deposition date:
2022-02-01
Original release date:
2023-02-08
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.; Lavrenova, V.; Ivchenkov, D.; Bashkirov, P.; Kot, E.; Mineev, K.; Arseniev, A.; Klinov, D.; Lazarev, V.. "The study of the interaction of cationic peptides from a medical leech with blood components as a first step to the systemic use of antimicrobial peptides for therapy of infectious diseases"  .

Assembly members:

Assembly members:
entity_1, polymer, 24 residues, 2678.292 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: RAVIYKIPYNAIASRWIIAP KKCX

Data sets:
Data typeCount
13C chemical shifts88
15N chemical shifts23
1H chemical shifts184

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11

Entities:

Entity 1, unit_1 24 residues - 2678.292 Da.

1   ARGALAVALILETYRLYSILEPROTYRASN
2   ALAILEALASERARGTRPILEILEALAPRO
3   LYSLYSCYSNH2

Samples:

sample_1: prok_02022 peptide 0.9 mM; dodecyl phosphocholine, [U-2H], 91.3 mM; sodium acetate buffer, [U-2H], 20 mM; sodium azide 0.01 % w/v; TCEP 2 mM

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

Experiments:

NameSampleSample stateSample conditions
NOESYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-13C-HSQC-TOCSYsample_1isotropicsample_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 - refinement, structure calculation

NMR spectrometers:

  • Bruker AVANCE 700 MHz
  • Bruker AVANCE III 600 MHz

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