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- PDB-2ler: Conotoxin pc16a -

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Basic information

Entry
Database: PDB / ID: 2ler
TitleConotoxin pc16a
ComponentsConotoxin pc16a
KeywordsTOXIN
Function / homologytoxin activity / extracellular region / Conotoxin pc16a
Function and homology information
Biological speciesConus pictus (invertebrata)
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average, model 5
AuthorsDyubankova, N. / Lescrinier, E. / Van Der Haegen, A. / Peigneur, S. / Tytgat, J.
CitationJournal: Peptides / Year: 2012
Title: Pc16a, the first characterized peptide from Conus pictus venom, shows a novel disulfide connectivity.
Authors: Van Der Haegen, A. / Peigneur, S. / Dyubankova, N. / Moller, C. / Mari, F. / Diego-Garcia, E. / Naude, R. / Lescrinier, E. / Herdewijn, P. / Tytgat, J.
History
DepositionJun 22, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Source and taxonomy

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Conotoxin pc16a


Theoretical massNumber of molelcules
Total (without water)1,2661
Polymers1,2661
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 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Conotoxin pc16a


Mass: 1265.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: venom / Source: (synth.) Conus pictus (invertebrata) / References: UniProt: P86942*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H NOESY
1312D 1H-13C HSQC

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Sample preparation

DetailsContents: 5 mg conotoxin pc16a, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 5 mg/mL / Component: conotoxin pc16a-1
Sample conditionspH: 6 / Pressure: ambient / Temperature: 283 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TOPSPINBruker Biospincollection
X-PLOR_NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR_NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 123 / NOE intraresidue total count: 103 / NOE long range total count: 3 / NOE medium range total count: 3 / NOE sequential total count: 14
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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