1C0Q

COMPLEX OF VANCOMYCIN WITH 2-ACETOXY-D-PROPANOIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.119 

wwPDB Validation 3D Report Full Report


This is version 1.6 of the entry. See complete history

Literature

Vancomycin binding to low-affinity ligands: delineating a minimum set of interactions necessary for high-affinity binding.

Loll, P.J.Kaplan, J.Selinsky, B.S.Axelsen, P.H.

(1999) J.Med.Chem. 42: 4714-4719

  • Primary Citation of Related Structures:  1C0R, 1QD8

  • PubMed Abstract: 
  • Bacterial resistance to vancomycin has been attributed to the loss of an intermolecular hydrogen bond between vancomycin and its peptidoglycan target when cell wall biosynthesis proceeds via depsipeptide intermediates rather than the usual polypeptid ...

    Bacterial resistance to vancomycin has been attributed to the loss of an intermolecular hydrogen bond between vancomycin and its peptidoglycan target when cell wall biosynthesis proceeds via depsipeptide intermediates rather than the usual polypeptide intermediates. To investigate the relative importance of this hydrogen bond to vancomycin binding, we have determined crystal structures at 1.0 A resolution for the vancomycin complexes with three ligands that mimic peptides and depsipeptides found in vancomycin-sensitive and vancomycin-resistant bacteria: N-acetylglycine, D-lactic acid, and 2-acetoxy-D-propanoic acid. These, in conjunction with structures that have been reported previously, indicate higher-affinity ligands elicit a structural change in the drug not seen with these low-affinity ligands. They also enable us to define a minimal set of drug-ligand interactions necessary to confer higher-affinity binding on a ligand. Most importantly, these structures point to factors in addition to the loss of an intermolecular hydrogen bond that must be invoked to explain the weaker affinity of vancomycin for depsipeptide ligands. These factors are important considerations for the design of vancomycin analogues to overcome vancomycin resistance.


    Organizational Affiliation

    Department of Pharmacology, University of Pennsylvania, 3620 Hamilton Walk, Philadelphia, Pennsylvania 19104, USA. loll@pharm.med.upenn.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VANCOMYCIN
A, B
7N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LAC
Query on LAC

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Download CCD File 
B
LACTIC ACID
C3 H6 O3
JVTAAEKCZFNVCJ-UWTATZPHSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
BGC
Query on BGC

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Download CCD File 
A, B
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
RER
Query on RER

Download SDF File 
Download CCD File 
A, B
(1R,3S,4S,5S)-3-amino-2,3,6-trideoxy-3-methyl-alpha-L-arabino-hexopyranose
VANCOSAMINE
C7 H15 N O3
OIJZDPGKNVKVBL-WNJXEPBRSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000204
Query on PRD_000204
A,BVANCOMYCINGlycopeptide / Antibiotic

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.119 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 28.400α = 90.00
b = 28.400β = 90.00
c = 65.730γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-93model building
SHELXL-93phasing
SHELXL-93refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-07-30
    Type: Initial release
  • Version 1.1: 2008-04-26
    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
  • Version 1.5: 2013-03-27
    Type: Structure summary
  • Version 1.6: 2013-04-10
    Type: Derived calculations