NMR structure of omega-agatoxin IVA in DPC micelles

> Summary

Summary for 2NDB

DescriptorOmega-agatoxin-Aa4a (1 entity in total)
Functional Keywordsneurotoxin, toxin
Biological sourceAgelenopsis aperta (North American funnel-web spider)
Cellular locationSecreted  P30288
Total number of polymer chains1
Total molecular weight5277.45
Ryu, J.H.,Kim, J.I. (deposition date: 2016-05-12, release date: 2017-09-13)
Primary citation
Ryu, J.H.,Jung, H.J.,Konishi, S.,Kim, H.H.,Park, Z.Y.,Kim, J.I.
Structure-activity relationships of omega-Agatoxin IVA in lipid membranes
Biochem. Biophys. Res. Commun., 482:170-175, 2017
PubMed: 27838299 (PDB entries with the same primary citation)
DOI: 10.1016/j.bbrc.2016.11.025
MImport into Mendeley
Experimental method

Structure validation

ClashscoreRamachandran outliersSidechain outliers2811.9%27.1%MetricValuePercentile RanksWorseBetterPercentile relative to all structuresPercentile relative to all NMR structures

More Asymmetric unit images

Molmil generated image of 2ndb
no rotation
Molmil generated image of 2ndb
rotated about x axis by 90°
Molmil generated image of 2ndb
rotated about y axis by 90°

> Structural details


Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
UniProt (P30288)
Agelenopsis aperta (North American funnel-web spider)Omega-AGTX-Aa4a, Omega-agatoxin IVA, Omega-Aga-IVA, Omega-agatoxin-4A

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains1
Total molecular weight5277.4
Non-Polymers*Number of molecules0
Total molecular weight0.0
All*Total molecular weight5277.4
*Water molecules are not included.

> Experimental details


Experimental method:SOLUTION NMR

Spectrometer IDSpectrometer makerSpectrometer modelSpectrometer typeSpectrometer field strength
1BrukerAvanceBruker Avance600


experiment idconditions idsolution idExperiment type
1112D 1H-1H TOCSY
3112D 1H-1H NOESY
4112D 1H-15N HSQC
5113D 1H-15N NOESY
6113D 1H-15N TOCSY

NMR Sample

conditions idNMR sample pHNMR sample pressureNMR sample temperature


Conformers Calculated Total Number100
Conformers Submitted Total Number20

> Functional details


Functional Information from GO Data


Functional Information from PDB Data

site_idNumber of ResiduesDetails

Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails

Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails

Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails

Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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