1GHG

CRYSTAL STRUCTURE OF VANCOMYCIN AGLYCON


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.98 Å
  • R-Value Free: 0.150 
  • R-Value Observed: 0.150 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

The Role of Sugar Residues in Molecular Recognition by Vancomycin

Kaplan, J.Korty, B.D.Axelsen, P.H.Loll, P.J.

(2001) J Med Chem 44: 1837

  • DOI: 10.1021/jm0005306
  • Primary Citation of Related Structures:  
    1GHG

  • PubMed Abstract: 
  • The sugar residues of the glycopeptide antibiotic vancomycin contribute to the cooperativity of ligand binding, thereby increasing ligand affinity and enhancing antimicrobial activity. To assess the structural basis for these effects, we determined a 0.98 A X-ray crystal structure of the vancomycin aglycon and compared it to structures of several intact vancomycin:ligand complexes ...

    The sugar residues of the glycopeptide antibiotic vancomycin contribute to the cooperativity of ligand binding, thereby increasing ligand affinity and enhancing antimicrobial activity. To assess the structural basis for these effects, we determined a 0.98 A X-ray crystal structure of the vancomycin aglycon and compared it to structures of several intact vancomycin:ligand complexes. The crystal structure reveals that the aglycon binds acetate anions and forms back-to-back dimeric complexes in a manner similar to that of intact vancomycin. However, the four independent copies of the aglycon in each asymmetric unit of the crystal exhibit a high degree of conformational heterogeneity. These results suggest that the sugar residues, in addition to enlarging and strengthening the dimer interface, provide steric constraints that limit the vancomycin molecule to a relatively small number of productive conformations.


    Organizational Affiliation

    Department of Pharmacology, University of Pennsylvania, 3620 Hamilton Walk, Philadelphia, Pennsylvania 19104, USA.



Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
VANCOMYCIN AGLYCONA, B, C, D7Amycolatopsis orientalisMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OMY
Query on OMY
A, B, C, DL-PEPTIDE LINKINGC9 H10 Cl N O4TYR
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 1
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000206
Query on PRD_000206
A, B, C, DVANCOMYCIN AGLYCONOligopeptide / Antibiotic Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.98 Å
  • R-Value Free: 0.150 
  • R-Value Observed: 0.150 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 29.48α = 90
b = 29.48β = 90
c = 74.27γ = 90
Software Package:
Software NamePurpose
SnBphasing
SHELXLrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-02-12
    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 1.5: 2017-10-04
    Changes: Refinement description