1DLZ

SOLUTION STRUCTURE OF THE CHANNEL-FORMER ZERVAMICIN IIB (PEPTAIBOL ANTIBIOTIC)


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: BEST 20 OUT OF 100 WITH CA BACKBONE RMSD NO LESS THAN 0.05 ANGSTROMS 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

NMR Structure of the Channel-Former Zervamicin Iib in Isotropic Solvents.

Balashova, T.A.Shenkarev, Z.O.Tagaev, A.A.Ovchinnikova, T.V.Raap, J.Arseniev, A.S.

(2000) FEBS Lett 466: 333

  • DOI: 10.1016/s0014-5793(99)01707-x
  • Primary Citation of Related Structures:  
    1DLZ

  • PubMed Abstract: 
  • Spatial structure of the membrane channel-forming hexadecapeptide, zervamicin IIB, was studied by NMR spectroscopy in mixed solvents of different polarity ranging from CDCl3/CD3OH (9:1, v/v) to CD3OH/H2O (1:1, v/v). The results show that in all solvents used the peptide has a very similar structure that is a bent amphiphilic helix with a mean backbone root mean square deviation (rmsd) value of ca ...

    Spatial structure of the membrane channel-forming hexadecapeptide, zervamicin IIB, was studied by NMR spectroscopy in mixed solvents of different polarity ranging from CDCl3/CD3OH (9:1, v/v) to CD3OH/H2O (1:1, v/v). The results show that in all solvents used the peptide has a very similar structure that is a bent amphiphilic helix with a mean backbone root mean square deviation (rmsd) value of ca. 0.3 A. Side chains of Trp1, Ile2, Gln3, Ile5 and Thr6 are mobile. The results are discussed in relation to the validity of the obtained structure to serve as a building block of zervamicin IIB ion channels.


    Organizational Affiliation

    Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, Moscow, Russia.



Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ZERVAMICIN IIBA17Emericellopsis salmosynnemataMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
AIB
Query on AIB
A L-PEPTIDE LINKINGC4 H9 N O2ALA
HYP
Query on HYP
A L-PEPTIDE LINKINGC5 H9 N O3PRO
PHL
Query on PHL
A L-PEPTIDE LINKINGC9 H13 N OPHE
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 1
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000159
Query on PRD_000159
AZervamicin IIBPeptaibol / Antibiotic Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: BEST 20 OUT OF 100 WITH CA BACKBONE RMSD NO LESS THAN 0.05 ANGSTROMS 
  • OLDERADO: 1DLZ Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-02-03
    Type: Initial release
  • Version 1.1: 2011-06-14
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-07-27
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 1.4: 2012-12-12
    Changes: Other