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- PDB-5ykl: Antimicrobial peptide AY1C designed from the skin secretion of Ch... -

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Basic information

Entry
Database: PDB / ID: 5ykl
TitleAntimicrobial peptide AY1C designed from the skin secretion of Chinese Odorous frogs
Componentsdesigned AY1C
KeywordsANTIMICROBIAL PROTEIN / CYANA 2.1
Biological speciesOdorrana andersonii (golden crossband frog)
MethodSOLUTION NMR / distance geometry
AuthorsPal, I. / Atreya, H.S. / Bhunia, A.
Funding support India, 1items
OrganizationGrant numberCountry
DSTDST1028 India
CitationJournal: Sci Rep / Year: 2019
Title: A Peptide-Nanoparticle System with Improved Efficacy against Multidrug Resistant Bacteria.
Authors: Pal, I. / Bhattacharyya, D. / Kar, R.K. / Zarena, D. / Bhunia, A. / Atreya, H.S.
History
DepositionOct 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: designed AY1C


Theoretical massNumber of molelcules
Total (without water)2,2661
Polymers2,2661
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2420 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100all calculated structures submitted
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide designed AY1C


Mass: 2265.869 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Designed antimicrobial peptide
Source: (synth.) Odorrana andersonii (golden crossband frog)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
141isotropic12D 1H-1H TOCSY
151isotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: lyophilized powder / Contents: 2 mM pepride, 90% H2O/10% D2O / Label: NA / Solvent system: 90% H2O/10% D2O
SampleConc.: 2 mM / Component: pepride / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 2 mM / Label: In LUV / pH: 6 / Pressure: 76 mmHg / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
XEASYBartels et al.chemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
XEASYBartels et al.peak picking
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 100 / Conformers submitted total number: 20

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