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- PDB-5zvf: Structure of [T9,K7]indolicidin, a non glycosylated analogue of i... -

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Basic information

Entry
Database: PDB / ID: 5zvf
TitleStructure of [T9,K7]indolicidin, a non glycosylated analogue of indolicidin
Componentsnon glycosylated analogue of Indolicidin
KeywordsANTIMICROBIAL PROTEIN / Antimicrobial Peptide
Function / homology
Function and homology information


Antimicrobial peptides / Neutrophil degranulation / defense response to fungus / lipopolysaccharide binding / antimicrobial humoral immune response mediated by antimicrobial peptide / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / innate immune response / extracellular space
Similarity search - Function
Cathelicidins signature 1. / Cathelicidin, conserved site / Cathelicidins signature 2. / Cathelicidin-like / Cathelicidin / Cystatin superfamily
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodSOLUTION NMR / simulated annealing
AuthorsDwivedi, R. / Aggarwal, P. / Kaur, K.J. / Bhavesh, N.S.
Funding support India, 1items
OrganizationGrant numberCountry
DST SR/S1/OC-63/2012 India
CitationJournal: Amino Acids / Year: 2019
Title: Design of therapeutically improved analogue of the antimicrobial peptide, indolicidin, using a glycosylation strategy.
Authors: Dwivedi, R. / Aggarwal, P. / Bhavesh, N.S. / Kaur, K.J.
History
DepositionMay 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Data collection / Database references
Category: citation / citation_author / pdbx_nmr_spectrometer
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 / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_nmr_spectrometer.model
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: non glycosylated analogue of Indolicidin


Theoretical massNumber of molelcules
Total (without water)1,8551
Polymers1,8551
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry, Mass of peptide is 1852.1395 Daltons
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2380 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide non glycosylated analogue of Indolicidin


Mass: 1855.258 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Antimicrobial peptide and derivative of Indolicidin
Source: (synth.) Bos taurus (cattle) / References: UniProt: P33046*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-1H TOCSY

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Sample preparation

DetailsType: micelle / Contents: 2 mM peptide, 90% H2O/10% D2O
Details: 10mM Phosphate Buffer pH 4.7 400mM dodecylphosphorylcholine - d38
Label: UL / Solvent system: 90% H2O/10% D2O
SampleConc.: 2 mM / Component: peptide / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0.03 mM / Ionic strength err: 0.001 / Label: 1 / pH: 4.7 / PH err: 0.05 / Pressure: 1 atm / Pressure err: 0.1 / Temperature: 310 K / Temperature err: 0.001

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500.15 MHz / Details: Avance III

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Processing

NMR software
NameVersionDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
TopSpin2.1Bruker Biospincollection
CARAKeller and Wuthrichpeak picking
CARAKeller and Wuthrichchemical shift calculation
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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