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 3.0 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: https://doi.org/10.1021/bi961017q
  • Primary Citation of Related Structures:  
    1DSR

  • 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 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   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RAMOPLANIN A217Actinoplanes sp.Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose
B
2N/A
Glycosylation Resources
GlyTouCan:  G53402KW
GlyCosmos:  G53402KW
GlyGen:  G53402KW
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FA7
Query on FA7

Download Ideal Coordinates CCD File 
C [auth A](2Z,4E)-7-methylocta-2,4-dienoic acid
C9 H14 O2
ZPJFGJWTSDWBST-BZDQXIRASA-N
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
AHB
Query on AHB
A
L-PEPTIDE LINKINGC4 H8 N2 O4ASN
ALO
Query on ALO
A
L-PEPTIDE LINKINGC4 H9 N O3THR
CHP
Query on CHP
A
L-PEPTIDE LINKINGC8 H8 Cl N O3GLY
Biologically Interesting Molecules (External Reference) 2 Unique
Entity ID: 1
IDChains NameType/Class2D Diagram3D Interactions
PRD_000222
Query on PRD_000222
A
RAMOPLANIN A2Lipoglycopeptide / Antibiotic
Entity ID: 2
IDChains NameType/Class2D Diagram3D Interactions
PRD_000222
Query on PRD_000222
B
RAMOPLANIN A2Lipoglycopeptide / Antibiotic
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



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-02-12
    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 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 3.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary