1C0Q

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.119 
  • R-Value Observed: 0.119 

wwPDB Validation   3D Report Full Report


This is version 2.0 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

  • DOI: 10.1021/jm990361t
  • Primary Citation of Related Structures:  
    1C0R, 1C0Q, 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 polypeptide intermediates ...

    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 LengthOrganismDetailsImage
VANCOMYCINA, B7Amycolatopsis orientalisMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
vancosamine-(1-2)-beta-D-glucopyranoseC, D2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G14263HU
GlyCosmos:  G14263HU
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LAC
Query on LAC

Download Ideal Coordinates CCD File 
H [auth B]LACTIC ACID
C3 H6 O3
JVTAAEKCZFNVCJ-UWTATZPHSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A], F [auth B], G [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OMY
Query on OMY
A, BL-PEPTIDE LINKINGC9 H10 Cl N O4TYR
Biologically Interesting Molecules (External Reference) 2 Unique
Entity ID: 1
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000204
Query on PRD_000204
A, BVancomycinGlycopeptide /  Antibiotic Ligand Interaction
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000204
Query on PRD_000204
C, DVancomycinGlycopeptide /  Antibiotic Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.119 
  • R-Value Observed: 0.119 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 28.4α = 90
b = 28.4β = 90
c = 65.73γ = 90
Software Package:
Software NamePurpose
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: 1999-07-30
    Type: Initial release
  • Version 1.1: 2008-04-26
    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: 2013-03-27
    Changes: Structure summary
  • Version 1.6: 2013-04-10
    Changes: Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Polymer sequence, Refinement description, Structure summary