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- PDB-6kn3: Structure of single disulfide peptide Czon1107-WT (minor conformer) -

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Entry
Database: PDB / ID: 6kn3
TitleStructure of single disulfide peptide Czon1107-WT (minor conformer)
ComponentsCzon1107-WT(Conformer B)
KeywordsNEUROPEPTIDE / nAChR antagonist NMR
Biological speciesConus zonatus (invertebrata)
MethodSOLUTION NMR / simulated annealing
AuthorsSarma, S.P. / Madhan Kumar, M.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)IISc Partnership Program India
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structure and allosteric activity of a single-disulfide conopeptide fromConus zonatusat human alpha 3 beta 4 and alpha 7 nicotinic acetylcholine receptors.
Authors: Mohan, M.K. / Abraham, N. / R P, R. / Jayaseelan, B.F. / Ragnarsson, L. / Lewis, R.J. / Sarma, S.P.
History
DepositionAug 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 27, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jun 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Czon1107-WT(Conformer B)


Theoretical massNumber of molelcules
Total (without water)1,1091
Polymers1,1091
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area100 Å2
ΔGint0 kcal/mol
Surface area1110 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)23 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Czon1107-WT(Conformer B)


Mass: 1109.324 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Conus zonatus (invertebrata)
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D DQF-COSY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-13C HSQC
141isotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: solution / Contents: 3.0 mM Czon1107-WT, 90% H2O/10% D2O / Label: 1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 3.0 mM / Component: Czon1107-WT / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0 Not defined / Ionic strength err: 0 / Label: 1 / pH: 7 / PH err: 0.05 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 0.3

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AVANCEBrukerAVANCE7002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
CcpNmr AnalysisCCPNpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 23

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