1DLZ | pdb_00001dlz

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

• PDB DOI: https://doi.org/10.2210/pdb1DLZ/pdb
• BMRB: 4601

• Classification: ANTIBIOTIC
• Organism(s): Emericellopsis salmosynnemata
• Mutation(s): No 


• Deposited: 1999-12-13 Released: 2000-02-03 
• Deposition Author(s): Balashova, T.A., Shenkarev, Z.O., Tagaev, A.A., Ovchinnikova, T.V., Raap, J., Arseniev, A.S.

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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 

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

• PubMed: 10682854 
• DOI: https://doi.org/10.1016/s0014-5793(99)01707-x
• Primary Citation 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. 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 1.82 kDa 
• Atom Count: 131 
• Modeled Residue Count: 17 
• Deposited Residue Count: 17 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ZERVAMICIN IIB	A	17	Emericellopsis salmosynnemata	Mutation(s): 0

Small Molecules

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AIB	A	L-PEPTIDE LINKING	C4 H9 N O2		ALA
DIV	A	D-PEPTIDE LINKING	C5 H11 N O2		--
HYP	A	L-PEPTIDE LINKING	C5 H9 N O3		PRO
PHL	A	L-PEPTIDE LINKING	C9 H13 N O		PHE

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000159	A	Zervamicin IIB	Peptaibol / Antibiotic

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 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-02-03 
Deposition Author(s): Balashova, T.A., Shenkarev, Z.O., Tagaev, A.A., Ovchinnikova, T.V., Raap, J., Arseniev, A.S.

Revision History  

• 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
• Version 1.5: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Experimental preparation, Structure summary