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- PDB-5z32: LPS bound solution NMR structure of WS2-VR18 -

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Basic information

Entry
Database: PDB / ID: 5z32
TitleLPS bound solution NMR structure of WS2-VR18
ComponentsVAL-ALA-ARG-GLY-TRP-GLY-ARG-LYS-CYS-PRO-LEU-PHE-GLY-LYS-ASN-LYS-SER-ARG
KeywordsANTIMICROBIAL PROTEIN / De novo designed peptide / Quantum dot conjugate / LPS bound structure / Antimicrobial activity
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsBhunia, A. / Mohid, S.A.
Funding support India, 1items
OrganizationGrant numberCountry
DST for Indo-Sweden Joint Project GrantDST/INT/SWD/VR/P-02/2014 India
CitationJournal: Colloids Surf B Biointerfaces / Year: 2019
Title: Application of tungsten disulfide quantum dot-conjugated antimicrobial peptides in bio-imaging and antimicrobial therapy.
Authors: Mohid, S.A. / Ghorai, A. / Ilyas, H. / Mroue, K.H. / Narayanan, G. / Sarkar, A. / Ray, S.K. / Biswas, K. / Bera, A.K. / Malmsten, M. / Midya, A. / Bhunia, A.
History
DepositionJan 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: citation / database_2 ...citation / database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2May 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: VAL-ALA-ARG-GLY-TRP-GLY-ARG-LYS-CYS-PRO-LEU-PHE-GLY-LYS-ASN-LYS-SER-ARG


Theoretical massNumber of molelcules
Total (without water)2,0661
Polymers2,0661
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1960 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 VAL-ALA-ARG-GLY-TRP-GLY-ARG-LYS-CYS-PRO-LEU-PHE-GLY-LYS-ASN-LYS-SER-ARG


Mass: 2066.479 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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 TOCSY
121isotropic12D trNOESY

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Sample preparation

DetailsType: solid
Contents: 0.5 mM VAL-ALA-ARG-GLY-TRP-GLY-ARG-LYS-CYS-PRO-LEU-PHE-GLY-LYS-ASN-LYS-SER-ARG, 90% H2O/10% D2O
Details: 2 mg WS2-VR18 peptide was dissolved in 1 ml Milli Q water to obtain 0.5 mM stock solution.
Label: WS2-VR18 / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM
Component: VAL-ALA-ARG-GLY-TRP-GLY-ARG-LYS-CYS-PRO-LEU-PHE-GLY-LYS-ASN-LYS-SER-ARG
Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0 Not defined / Label: Peptide aqueous solution / pH: 4.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
TopSpin3.1Bruker Biospinprocessing
Sparky3.114Goddardchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
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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