1DSR

Peptide antibiotic, NMR, 6 structures


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 450 
  • Conformers Submitted: 
  • Selection Criteria: ENERGY MINIMIZED SNAPSHOT EVERY 75 PS 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

3D Structure of Ramoplanin: A Potent Inhibitor of Bacterial Cell Wall Synthesis.

Kurz, M.Guba, W.

(1996) Biochemistry 35: 12570

  • DOI: 10.1021/bi961017q

  • PubMed Abstract: 
  • The 3D structure of ramoplanin was studied by NMR spectroscopy in aqueous solution. A total of 320 interproton distances were determined from a NOESY spectrum and were used as restraints in distance geometry calculations. A structural refinement was ...

    The 3D structure of ramoplanin was studied by NMR spectroscopy in aqueous solution. A total of 320 interproton distances were determined from a NOESY spectrum and were used as restraints in distance geometry calculations. A structural refinement was carried out by molecular dynamics calculations in a solvent box. The structure of ramoplanin is characterized by two antiparallel beta-strands which are formed by the residues 2-7 and 10-14, respectively. The beta-strands are connected by six intramolecular hydrogen bonds and a reverse beta-turn which is formed by Thr8 and Phe9 (in positions i+1 and i+2, respectively). Residues 2 and 14 are connected by a loop consisting of Leu15, Ala16, Chp17, and the side chain of Asn2. Although residues 14-17 show the formation of a beta-turn, only the N-terminal end of the turn is directly connected to one of the beta-strands (Gly14), whereas the C-terminal end (Chp17) is linked via the side chain of Asn2. The 3D conformation of ramoplanin is also stabilized by a hydrophobic cluster of the aromatic sidechains of the residues 3, 9, and 17. This hydrophobic collapse leads to a U-shaped topology of the beta-shee: with the beta-turn at one end and the loop at the other end. The structure found for ramoplanin differs corsiderably from the published structure of ramoplanose which might be due to a smaller number of NOE distance restraints used in the previous study.


    Organizational Affiliation

    Central Pharma Research, Frankfurt am Main, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RAMOPLANIN A2
A
17N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FA7
Query on FA7

Download SDF File 
Download CCD File 
A
(2Z,4E)-7-methylocta-2,4-dienoic acid
C9 H14 O2
ZPJFGJWTSDWBST-BZDQXIRASA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000222
Query on PRD_000222
ARAMOPLANIN A2Lipoglycopeptide / Antibiotic

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Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 450 
  • Conformers Submitted: 
  • Selection Criteria: ENERGY MINIMIZED SNAPSHOT EVERY 75 PS 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1996-07-05 
  • Released Date: 1997-02-12 
  • Deposition Author(s): Kurz, M., Guba, W.

Revision History 

  • Version 1.0: 1997-02-12
    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