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Basic information

Entry
Database: PDB / ID: 2l5r
TitleConformational and membrane interactins studies of antimicrobial peptide Alyteserin-1C
ComponentsAntimicrobial peptide Alyteserin-1C
KeywordsANTIMICROBIAL PROTEIN / alpha helix
Function / homologyother organism cell membrane / defense response to bacterium / innate immune response / extracellular region / membrane / Alyteserin-1c
Function and homology information
Biological speciesAlytes obstetricans (midwife toad)
MethodSOLUTION NMR / simulated annealing
AuthorsSubasinghage, A.P. / Hewage, C.M. / Conlon, M.
CitationJournal: Biochim.Biophys.Acta / Year: 2011
Title: Conformational and membrane interaction studies of the antimicrobial peptide alyteserin-1c and its analogue [E4K]alyteserin-1c.
Authors: Subasinghage, A.P. / O'Flynn, D. / Conlon, J.M. / Hewage, C.M.
History
DepositionNov 3, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antimicrobial peptide Alyteserin-1C


Theoretical massNumber of molelcules
Total (without water)2,2711
Polymers2,2711
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Antimicrobial peptide Alyteserin-1C


Mass: 2270.714 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Alytes obstetricans (midwife toad) / References: UniProt: H0USY4*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY

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Sample preparation

DetailsContents: 290 mM DHPC, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 290 mM / Component: DHPC
Sample conditionsPressure: ambient / Temperature: 307 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2Bruker Biospincollection
TopSpin2Bruker Biospinprocessing
TopSpin2Bruker Biospindata analysis
Sparky3.114Goddardpeak picking
Sparky3.114Goddardchemical shift assignment
CYANA2Guntert, Mumenthaler and Wuthrichstructure solution
SYBYL6.8.1Triposrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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