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- PDB-1yz2: Solution structure of Am2766 -

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Basic information

Entry
Database: PDB / ID: 1yz2
TitleSolution structure of Am2766
ComponentsDelta-conotoxin Am 2766
KeywordsTOXIN / Delta conotoxin / molluscivorous snail / inhibitory cysteine knot motif / 15 structures
Function / homologyConotoxin, delta-type, conserved site / Delta-conotoxin family signature. / sodium channel inhibitor activity / : / toxin activity / extracellular region / Delta-conotoxin Am2766
Function and homology information
Biological speciesConus amadis (invertebrata)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSarma, S.P. / Kumar, G.S. / Sudarslal, S. / Iengar, P. / Sikdar, S.K. / Krishnan, K.S. / Balaram, P.
CitationJournal: CHEM.BIODIVERS. / Year: 2005
Title: Solution Structure of delta-Am2766: A Highly Hydrophobic delta-Conotoxin from Conus amadis That Inhibits Inactivation of Neuronal Voltage-Gated Sodium Channels
Authors: Sarma, S.P. / Kumar, G.S. / Sudarslal, S. / Iengar, P. / Ramasamy, P. / Sikdar, S.K. / Krishnan, K.S. / Balaram, P.
History
DepositionFeb 26, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Database references / Derived calculations
Category: pdbx_nmr_representative / pdbx_nmr_software ...pdbx_nmr_representative / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _pdbx_nmr_representative.selection_criteria / _pdbx_nmr_software.authors ..._pdbx_nmr_representative.selection_criteria / _pdbx_nmr_software.authors / _pdbx_nmr_software.classification / _pdbx_nmr_software.name / _pdbx_nmr_software.version / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Delta-conotoxin Am 2766


Theoretical massNumber of molelcules
Total (without water)2,7721
Polymers2,7721
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area120 Å2
ΔGint1 kcal/mol
Surface area1940 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 50structures with the least restraint violations
RepresentativeModel #11

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Components

#1: Protein/peptide Delta-conotoxin Am 2766


Mass: 2772.206 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Conus amadis (invertebrata) / Secretion: venom / References: UniProt: P60179

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D NOESY
1312D TOCSY
1412D ROESY
1512D 1H-13C HSQC
1622D TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
12-3mM delta Am276699% CD3OH
22-3mM delta Am276699% CD3OD
Sample conditionsPressure: Ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS6001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1AVARIANrefinement
X-PLOR-NIH2.9.1SCHWIETERSrefinement
XwinNMR2.6structure solution
NMRPIPE VERSION2.3structure solution
ANSIG3.3structure solution
X-PLOR-NIH2.9.1structure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 15

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