1AY3

Nodularin from Nodularia spumigena

  • Classification: TOXIN
  • Mutation(s): 

  • Deposited: 1997-11-14 Released: 1999-08-16 
  • Deposition Author(s): Annila, A.J.

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 27 
  • Selection Criteria: RESTRAINT VIOLATIONS 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Solution structure of nodularin. An inhibitor of serine/threonine-specific protein phosphatases.

Annila, A.Lehtimaki, J.Mattila, K.Eriksson, J.E.Sivonen, K.Rantala, T.T.Drakenberg, T.

(1996) J.Biol.Chem. 271: 16695-16702


  • PubMed Abstract: 
  • The three-dimensional solution structure of nodularin was studied by NMR and molecular dynamics simulations. The conformation in water was determined from the distance and dihedral data by distance geometry and refined by iterative relaxation matrix ...

    The three-dimensional solution structure of nodularin was studied by NMR and molecular dynamics simulations. The conformation in water was determined from the distance and dihedral data by distance geometry and refined by iterative relaxation matrix analysis. The cyclic backbone adopts a well defined conformation but the remote parts of the side chains of arginine as well as the amino acid derivative Adda have a large spatial dispersion. For the unusual amino acids the partial charges were calculated and nodularin was subjected to molecular dynamic simulations in water. A good agreement was found between experimental and computational data with hydrogen bonds, solvent accessibility, molecular motion, and conformational exchange. The three-dimensional structure resembles very closely that of microcystin-LR in the chemically equivalent segment. Therefore, it is expected that the binding of both microcystins and nodularins to serine/threonine-specific protein phosphatases is similar on an atomic level.


    Organizational Affiliation

    VTT Chemical Technology, P. O. Box 1401, FIN-02044 VTT, Finland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PEPTIDIC TOXIN NODULARIN
A
5N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
MFD
Query on MFD
A
NON-POLYMERC20 H29 N O3

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MDH
Query on MDH
A
PEPTIDE LINKINGC5 H9 N O2

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FGA
Query on FGA
A
D-gamma-peptide, C-delta linkingC5 H9 N O4

--

ACB
Query on ACB
A
D-beta-peptide, C-gamma linkingC5 H9 N O4

--

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 27 
  • Selection Criteria: RESTRAINT VIOLATIONS 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1997-11-14 
  • Released Date: 1999-08-16 
  • Deposition Author(s): Annila, A.J.

Revision History 

  • Version 1.0: 1999-08-16
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-07-27
    Type: Database references, Derived calculations, Non-polymer description, Source and taxonomy