1XT7

Daptomycin NMR Structure


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

NMR Structure Determination and Calcium Binding Effects of Lipopeptide Antibiotic Daptomycin

Ball, L.-J.Goult, C.M.Donarski, J.A.Micklefield, J.Ramesh, V.

(2004) Org.Biomol.Chem. 2: 1872

  • DOI: 10.1039/b402722a

  • PubMed Abstract: 
  • Daptomycin is an acidic lipopeptide antibiotic, whose three-dimensional structure and mechanism of action is currently unknown. Recently daptomycin, trade name Cubicin, was approved as a drug for the treatment of skin-related infections (M. Larkin La ...

    Daptomycin is an acidic lipopeptide antibiotic, whose three-dimensional structure and mechanism of action is currently unknown. Recently daptomycin, trade name Cubicin, was approved as a drug for the treatment of skin-related infections (M. Larkin Lancet, 2003, 3, 677) and became the first antibiotic of its class to be used in the clinic (A. Raja et al., Nature Rev. Drug Discov., 2003, 2, 943-944). We have carried out a systematic high field NMR study of daptomycin and its binding to calcium ions which is essential for antibiotic activity. In this first report, we demonstrate the sequence-specific resonance assignment of daptomycin under resolved NMR measurement conditions. In addition to this, we have determined the 3D structure of apo-daptomycin and demonstrated a 1 : 1 stoichiometry on the binding to calcium ions. We have also demonstrated that the binding of calcium ions does not result in major conformational changes, but does induce aggregation. This may be an important factor in the mode of action of daptomycin.


    Organizational Affiliation

    Department of Chemistry, University of Manchester Institute of Science and Technology, PO Box 88, Manchester, UKM60 1QD.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DAPTOMYCIN
A
13N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DKA
Query on DKA

Download SDF File 
Download CCD File 
A
DECANOIC ACID
C10 H20 O2
GHVNFZFCNZKVNT-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000217
Query on PRD_000217
ADaptomycinCyclic lipopeptide / Antibiotic

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Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-16
    Type: Initial release
  • Version 1.1: 2011-06-14
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-07-27
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 1.4: 2012-12-12
    Type: Other