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- PDB-1agg: THE SOLUTION STRUCTURE OF OMEGA-AGA-IVB, A P-TYPE CALCIUM CHANNEL... -

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Basic information

Entry
Database: PDB / ID: 1agg
TitleTHE SOLUTION STRUCTURE OF OMEGA-AGA-IVB, A P-TYPE CALCIUM CHANNEL ANTAGONIST FROM THE VENOM OF AGELENOPSIS APERTA
ComponentsOMEGA-AGATOXIN-IVB
KeywordsNEUROTOXIN / P-TYPE CALCIUM CHANNEL ANTAGONIST
Function / homology
Function and homology information


host cell presynaptic membrane / ion channel inhibitor activity / calcium channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Spider toxin / Spider toxin / Omega-AgatoxinV - #10 / Omega-AgatoxinV / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Biological speciesAgelenopsis aperta (spider)
MethodSOLUTION NMR
AuthorsReily, M.D. / Thanabal, V. / Adams, M.E.
Citation
Journal: J.Biomol.NMR / Year: 1995
Title: The solution structure of omega-Aga-IVB, a P-type calcium channel antagonist from venom of the funnel web spider, Agelenopsis aperta.
Authors: Reily, M.D. / Thanabal, V. / Adams, M.E.
#1: Journal: Nat.Struct.Biol. / Year: 1994
Title: Structure-Activity Relationships for P-Type Calcium Channel Selective Omega-Agatoxins
Authors: Reily, M.D. / Holub, K.E. / Gray, W.R. / Norris, T.M. / Adams, M.E.
#2: Journal: Mol.Pharmacol. / Year: 1993
Title: Structure and Properties of Omega-Aga-Ivb, a New Antagonist of P-Type Calcium Channels
Authors: Adams, M.E. / Mintz, I.M. / Reily, M.D. / Thanabal, V. / Bean, B.P.
History
DepositionNov 3, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 5, 2014Group: Atomic model
Revision 1.4Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OMEGA-AGATOXIN-IVB


Theoretical massNumber of molelcules
Total (without water)5,2871
Polymers5,2871
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)24 / -
Representative

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Components

#1: Protein/peptide OMEGA-AGATOXIN-IVB / OMEGA-AGA-IVB


Mass: 5287.132 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Agelenopsis aperta (spider) / References: UniProt: P37045
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Processing

NMR softwareName: DGII, DISCOVER / Developer: BIOSYM TECHNOLOGIES / Classification: refinement
RefinementSoftware ordinal: 1
Details: THE 3 N-TERMINAL AND 9 C-TERMINAL AMINO ACIDS ARE HIGHLY DISORDERED. DGII STRUCTURES WERE GENERATED WITH NOE, OMEGA-TORSION AND PHI-TORSION CONSTRAINTS AND A MINIMIZATION/DYNAMICS PROTOCOL ...Details: THE 3 N-TERMINAL AND 9 C-TERMINAL AMINO ACIDS ARE HIGHLY DISORDERED. DGII STRUCTURES WERE GENERATED WITH NOE, OMEGA-TORSION AND PHI-TORSION CONSTRAINTS AND A MINIMIZATION/DYNAMICS PROTOCOL WAS USED TO FURTHER REFINE THE DISTANCE GEOMETRY STRUCTURES. THE PROTOCOL CONSISTED OF 100 STEPS OF STEEPEST DESCENTS FOLLOWED BY 500 STEPS OF CONJUGATE GRADIENT MINIMIZATION WITHOUT CONSTRAINTS. ALL CONSTRAINTS WERE APPLIED AND EACH STRUCTURE SUBJECTED TO 500 STEPS OF CONJUGATE GRADIENT MINIMIZATION, 5 PS OF 300K MOLECULAR DYNAMICS, 500 STEPS OF CONJUGATE GRADIENT AND 100 STEEPEST DESCENTS MINIMIZATION. SOME MODELS WILL CONTAIN RESIDUES THAT HAVE UNFAVORABLE CONFORMATIONS, TYPICALLY IN THE DISORDERED REGIONS.
NMR ensembleConformers submitted total number: 24

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