1W9N | pdb_00001w9n

Isolation and characterization of epilancin 15X, a novel antibiotic from a clinical strain of Staphylococcus epidermidis

• PDB DOI: https://doi.org/10.2210/pdb1W9N/pdb

• Classification: ANTIBIOTIC
• Organism(s): Staphylococcus epidermidis
• Mutation(s): No 


• Deposited: 2004-10-14 Released: 2005-04-01 
• Deposition Author(s): Ekkelenkamp, M., Hanssen, M.G.M., Hsu, S.-T.D., de Jong, A., Milatovic, D., Verhoef, J., van Nuland, N.A.J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: LEAST TOTAL ENERGY 

Literature

Isolation and structural characterization of epilancin 15X, a novel lantibiotic from a clinical strain of Staphylococcus epidermidis.

Ekkelenkamp, M.B., Hanssen, M., Danny Hsu, S.T., de Jong, A., Milatovic, D., Verhoef, J., van Nuland, N.A.

(2005) FEBS Lett 579: 1917-1922

• PubMed: 15792796 
• DOI: https://doi.org/10.1016/j.febslet.2005.01.083
• Primary Citation Related Structures: 
  1W9N


• PubMed Abstract: 
  

  The potential application of lantibiotics as food-preserving agents and more recently as antibiotics has strongly increased the interest in these antibacterial peptides. Here, we report the elucidation of the primary and three-dimensional structures of the novel lantibiotic epilancin 15X from Staphylococcus epidermidis using high-resolution nuclear magnetic resonance spectroscopy and tandem mass spectrometry. The molecule contains ten post-translationally modified amino acids, three lanthionine ring structures and a hydroxy-propionyl N-terminal moiety. The primary and tertiary structure and the distribution of positive charges are closely similar to the previously identified lantibiotic epilancin K7, most likely indicative of a common mode of action.

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Organizational Affiliation: 
• University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 3.19 kDa 
• Atom Count: 222 
• Modeled Residue Count: 31 
• Deposited Residue Count: 31 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EPILANCIN 15X	A	31	Staphylococcus epidermidis	Mutation(s): 0
UniProt
Find proteins for P86047 (Staphylococcus epidermidis) Explore P86047  Go to UniProtKB:  P86047

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DAL	A	D-PEPTIDE LINKING	C3 H7 N O2		--
DBB	A	D-PEPTIDE LINKING	C4 H9 N O2		--
DBU	A	PEPTIDE LINKING	C4 H7 N O2		THR
DHA	A	PEPTIDE LINKING	C3 H5 N O2		SER

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000196	A	EPILANCIN 15X	Polypeptide / Lantibiotic

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: LEAST TOTAL ENERGY 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-04-01 
Deposition Author(s): Ekkelenkamp, M., Hanssen, M.G.M., Hsu, S.-T.D., de Jong, A., Milatovic, D., Verhoef, J., van Nuland, N.A.J.

Revision History  

• Version 1.0: 2005-04-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Structure summary, Version format compliance
• Version 1.2: 2012-11-30
  Changes: Other
• Version 1.3: 2018-05-02
  Changes: Data collection, Database references
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations, Other
• Version 3.0: 2024-05-01
  Changes: Polymer sequence