2DDE | pdb_00002dde

Structure of cinnamycin complexed with lysophosphatidylethanolamine

• PDB DOI: https://doi.org/10.2210/pdb2DDE/pdb

• Classification: ANTIBIOTIC
• Organism(s): Streptomyces griseoverticillatus
• Mutation(s): No 


• Deposited: 2006-01-27 Released: 2006-02-21 
• Deposition Author(s): Hosoda, K., Ohya, M., Kohno, T., Maeda, T., Endo, S., Wakamatsu, K.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Structure determination of an immunopotentiator peptide, cinnamycin, complexed with lysophosphatidylethanolamine by 1H-NMR1.

Hosoda, K., Ohya, M., Kohno, T., Maeda, T., Endo, S., Wakamatsu, K.

(1996) J Biochem 119: 226-230

• PubMed: 8882709 
• DOI: https://doi.org/10.1093/oxfordjournals.jbchem.a021226
• Primary Citation Related Structures: 
  2DDE


• PubMed Abstract: 
  

  The three-dimensional structure of a complex of cinnamycin, a 19-amino acid residue immunopotentiator peptide, and lysophosphatidylethanolamine was determined by 1H-NMR. The complex was cylindrical in shape, 11 A in diameter and 26 A in length, excluding the acyl chain of the phospholipid. The peptide had a hydrophobic pocket surrounded by residues Phe-7 through Ala(S)-14 to bind to the head group of the ligand. Fitting of the head group to the hydrophobic pocket was so good that other than a glycerophosphoethanolamine head group would be unable to fit the pocket. The goodness of the fitting is compatible with the strict specificity of ligand binding of the peptide.

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Organizational Affiliation: 
• Department of Biochemical Sciences, Gunma University.

Biological Assembly 1  

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

Biological assembly 1 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 2.33 kDa 
• Atom Count: 158 
• Modeled Residue Count: 19 
• Deposited Residue Count: 19 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LANTIBIOTIC CINNAMYCIN	A	19	Streptomyces griseoverticillatus	Mutation(s): 0
UniProt
Find proteins for P29827 (Streptomyces griseoverticillatus) Explore P29827  Go to UniProtKB:  P29827

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LSP	B [auth A]	(7S)-4,7-DIHYDROXY-10-OXO-3,5,9-TRIOXA-4-PHOSPHAUNDECAN-1-AMINIUM 4-OXIDE C7 H17 N O7 P CWRILEGKIAOYKP-ZETCQYMHSA-O

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
BH2	A	L-PEPTIDE LINKING	C4 H7 N O5		ASP
DAL	A	D-PEPTIDE LINKING	C3 H7 N O2		--
DBB	A	D-PEPTIDE LINKING	C4 H9 N O2		--

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000195	A	Cinnamycin	Polypeptide / Lantibiotic

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-02-21 
Deposition Author(s): Hosoda, K., Ohya, M., Kohno, T., Maeda, T., Endo, S., Wakamatsu, K.

Revision History  

• Version 1.0: 2006-02-21
  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: 2019-11-06
  Changes: Data collection, Database references, Derived calculations
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations
• Version 3.0: 2024-07-10
  Changes: Polymer sequence
• Version 3.1: 2024-11-06
  Changes: Structure summary