BMRB Entry 16817

Name: Solution structure of dermcidin-1L, a human antibiotic peptide
Published: 2010-06-15

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PDB ID: 2ksg
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR16817
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution structure of dermcidin-1L, a human antibiotic peptide

Deposition date:

2010-03-31

Original release date:

2010-06-15

Authors:

Jung, Hyun Ho; Yang, Sung-Tae; Kim, Jae Il

Citation:

Citation: Jung, Hyun Ho; Yang, Sung-Tae; Sim, Ji-Yeong; Lee, Seungkyu; Lee, Ju Yeon; Kim, Ha Hyung; Shin, Song Yub; Kim, Jae Il. "Analysis of the solution structure of the human antibiotic peptide dermcidin and its interaction with phospholipid vesicles." BMB Rep. 43, 362-368 (2010).
PubMed: 20510021

Assembly members:

Assembly members:
dermcidin-1L, polymer, 48 residues, 4826.549 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET31.b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
dermcidin-1L: SSLLEKGLDGAKKAVGGLGK LGKDAVEDLESVGKGAVHDV KDVLDSVL

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
15N chemical shifts	47
1H chemical shifts	297

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	dermcidin-1L	1

Entities:

Entity 1, dermcidin-1L 48 residues - 4826.549 Da.

1

SER

LEU

GLU

LYS

GLY

LEU

ASP

GLY

2

ALA

LYS

ALA

VAL

GLY

LEU

GLY

LYS

3

LEU

GLY

LYS

ASP

ALA

VAL

GLU

ASP

LEU

GLU

4

SER

VAL

GLY

LYS

GLY

ALA

VAL

HIS

ASP

VAL

5

LYS

ASP

VAL

LEU

ASP

SER

VAL

LEU

Samples:

sample_1: TFE, [U-99% 2H], 50%; D2O, [U-99% 2H], 10%; H2O 40%

sample_conditions_1: pH: 4.2; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
3D HNHA	sample_1	isotropic	sample_conditions_1

Software:

CNS, Brunger A. T. et.al. - refinement

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

NMR spectrometers:

Bruker Avance 600 MHz

PDB	2KSG 2YMK
GB	AAH62682 AAH69108 AAK94785 AAL18349 AAL25801
REF	NP_001287783 NP_444513 XP_001170688 XP_003807608 XP_004053332
SP	P81605
AlphaFold	P81605