1HHZ

Deglucobalhimycin in complex with cell wall pentapeptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.99 Å
  • R-Value Free: 0.140 
  • R-Value Observed: 0.107 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.4 of the entry. See complete history


Literature

Structures of Glycopeptide Antibiotics with Peptides that Model Bacterial Cell-Wall Precursors

Lehmann, C.Bunkoczi, G.Vertesy, L.Sheldrick, G.M.

(2002) J Mol Biol 318: 723

  • DOI: https://doi.org/10.1016/S0022-2836(02)00146-8
  • Primary Citation of Related Structures:  
    1GO6, 1HHU, 1HHY, 1HHZ

  • PubMed Abstract: 

    The vancomycin-related antibiotics balhimycin and degluco-balhimycin have been crystallized in complexes with di-, tri- and pentapeptides that emulate bacterial cell-wall precursors, and four structures determined at atomic resolution (<1 A). In addition to the features expected from previous structural and spectroscopic studies, two new motifs were observed that may prove important in the design of antibiotics modified to overcome bacterial resistance. A changed binding mode was found in two dipeptide complexes, and a new type of face-to-face oligomerization (in addition to the well-established back-to-back dimerization) was seen when the model peptide reaches a critical fraction of the size of the cell-wall precursor pentapeptide. The extensive interactions involving both antibiotic and peptide molecules in this interface should appreciably enhance the kinetic and thermodynamic stability of the complexes. In the pentapeptide complex, the relative positions of the peptides are close to those required for d-Ala elimination, so this structure may provide a realistic model for the prevention of the enzyme-catalyzed cell-wall crosslinking by antibiotic binding.


  • Organizational Affiliation

    Lehrstuhl für Strukturchemie, Institute für Anorganische Chemie, Universität Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DEGLUCOBALHIMYCIN
A, B, C
7Amycolatopsis sp.Mutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CELL WALL PEPTIDE
D, E, F
5synthetic constructMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.99 Å
  • R-Value Free: 0.140 
  • R-Value Observed: 0.107 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.29α = 90
b = 48.29β = 90
c = 39.3γ = 120
Software Package:
Software NamePurpose
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-09-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Structure summary, Version format compliance
  • Version 1.2: 2012-07-25
    Changes: Atomic model, Derived calculations, Non-polymer description, Other
  • Version 1.3: 2012-11-30
    Changes: Other
  • Version 2.0: 2019-04-24
    Changes: Advisory, Data collection, Derived calculations, Other, Polymer sequence
  • Version 2.1: 2019-07-10
    Changes: Data collection
  • Version 2.2: 2019-07-24
    Changes: Data collection
  • Version 2.3: 2019-10-09
    Changes: Data collection, Other, Source and taxonomy
  • Version 2.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations