1CCQ

NMR STRUCTURE WITH TIGHTLY BOUND WATER MOLECULES OF CYTOTOXIN II (CARDIOTOXIN) FROM NAJA NAJA OXIANA IN AQUEOUS SOLUTION (MINOR FORM).


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 220 
  • Conformers Submitted: 20 
  • Selection Criteria: LEAST RESTRAINT VIOLATION (TARGET FUNCTION VALUE) 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Two forms of cytotoxin II (cardiotoxin) from Naja naja oxiana in aqueous solution: spatial structures with tightly bound water molecules.

Dementieva, D.V.Bocharov, E.V.Arseniev, A.S.

(1999) Eur.J.Biochem. 263: 152-162

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 1H-NMR spectroscopy data, such as NOE intraprotein and (bound water)/protein contacts, 3J coupling constants and deuterium exchange rates were used to determine the in-solution spatial structure of cytotoxin II from Naja naja oxiana snake venom (CTII ...

    1H-NMR spectroscopy data, such as NOE intraprotein and (bound water)/protein contacts, 3J coupling constants and deuterium exchange rates were used to determine the in-solution spatial structure of cytotoxin II from Naja naja oxiana snake venom (CTII). Exploiting information from two 1H-NMR spectral components, shown to be due to cis/trans isomerization of the Val7-Pro8 peptide bond, spatial structures of CTII minor and major forms (1 : 6) were calculated using the torsion angle dynamics algorithm of the DYANA program and then energy refined using the FANTOM program. Each form, major and minor, is represented by 20 resulting conformers, demonstrating mean backbone rmsd values of 0.51 and 0.71 A, respectively. Two forms of CTII preserve the structural skeleton as three large loops, including two beta-sheets with bend regions, and demonstrate structural differences at loop I, where cis/trans isomerization occurs. The CTII side-chain distribution constitutes hydrophilic and hydrophobic belts around the protein, alternating in the trend of the three main loops. Because of the Omega-shaped backbone, formed in participation with two bound water molecules, the tip of loop II bridges the tips of loops I and III. This ensures the continuity of the largest hydrophobic belt, formed with the residues of these tips. Comparison revealed pronounced differences in the spatial organization of the tips of the three main loops between CTII and previous structures of homologous cytotoxins (cardiotoxins) in solution.


    Related Citations: 
    • Secondary Structure and Conformational Heterogeneity of Cytotoxin II from Naja Naja Oxiana
      Dementieva, D.V.,Utkin Yu, N.,Arseniev, A.S.
      (1996) RUSS.J.BIOORGANIC CHEM. V.: 289


    Organizational Affiliation

    Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (CYTOTOXIN 2)
A
60Naja oxianaMutation(s): 0 
Find proteins for P01441 (Naja oxiana)
Go to UniProtKB:  P01441
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 220 
  • Conformers Submitted: 20 
  • Selection Criteria: LEAST RESTRAINT VIOLATION (TARGET FUNCTION VALUE) 
  • Olderado: 1CCQ Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-06-29
    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: 2017-11-29
    Type: Derived calculations