1DTK

THE NMR SOLUTION STRUCTURE OF DENDROTOXIN K FROM THE VENOM OF DENDROASPIS POLYLEPIS POLYLEPIS


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 20 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Nuclear magnetic resonance solution structure of dendrotoxin K from the venom of Dendroaspis polylepis polylepis.

Berndt, K.D.Guntert, P.Wuthrich, K.

(1993) J Mol Biol 234: 735-750

  • DOI: 10.1006/jmbi.1993.1623
  • Primary Citation of Related Structures:  
    1DTK

  • PubMed Abstract: 
  • The solution structure of dendrotoxin K (Toxin K), a protein consisting of one polypeptide chain with 57 residues purified from the venom of the black mamba, Dendroaspis polylepis polylepis, was determined by nuclear magnetic resonance (NMR) spectros ...

    The solution structure of dendrotoxin K (Toxin K), a protein consisting of one polypeptide chain with 57 residues purified from the venom of the black mamba, Dendroaspis polylepis polylepis, was determined by nuclear magnetic resonance (NMR) spectroscopy. On the basis of virtually complete sequence-specific 1H NMR assignments, including individual assignments for 38 pairs of diastereotopic substituents and side-chain amide protons, a total of 818 nuclear Overhauser effect distance constraints and 123 dihedral angle constraints were identified. Using this input, the solution structure of Toxin K was calculated with the program DIANA, and refined by restrained energy-minimization with a modified version of the program AMBER. The average root-mean-square deviation (r.m.s.d.) relative to the mean atomic co-ordinates of the 20 conformers selected to represent the solution structure is 0.31 A for all backbone atoms N, C alpha and C', and 0.90 A for all heavy-atoms of residues 2 to 56. The solution structure of Toxin K is very similar to the solution structure of the basic pancreatic trypsin inhibitor (BPTI) and the X-ray crystal structure of the alpha-dendrotoxin from Dendroaspis angusticeps (alpha-DTX), with r.m.s.d. values of 1.31 A and 0.92 A, respectively, for the backbone atoms of residues 2 to 56. Some local structural differences between Toxin K and BPTI are directly related to the fact that intermolecular interactions with two of the four internal molecules of hydration water in BPTI are replaced by intramolecular hydrogen bonds in Toxin K.


    Related Citations: 
    • Assignment of the 1H Nuclear Magnetic Resonance Spectrum of the Trypsin Inhibitor Homologue K from Dendroaspis Polylepis Polylepis: Two-Dimensional Nuclear Magnetic Resonance at 360 and 500 Mhz
      Keller, R.M., Baumann, R., Hunziker-Kwik, E-H., Joubert, F.J., Wuthrich, K.
      (1983) J Mol Biol 163: 623
    • Evolutionary Conservation and Variation of Protein Folding Pathways: Two Protease Inhibitor Homologues from Black Mamba Vernom
      Hollecker, M., Creighton, T.E.
      (1983) J Mol Biol 168: 409
    • Protease Inhibitors as Snake Venom Toxins
      Strydom, D.J.
      (1973) Nature New Biol 247: 88

    Organizational Affiliation

    Institut für Molekularbiologie und Biophysik Eidgenössische Technische Hochschule-Hönggerberg, Zürich, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DENDROTOXIN KA57Dendroaspis polylepis polylepisMutation(s): 0 
Find proteins for P00981 (Dendroaspis polylepis polylepis)
Explore P00981 
Go to UniProtKB:  P00981
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 20 
  • OLDERADO: 1DTK Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance