3RUM

New strategy to analyze structures of glycopeptide antibiotic-target complexes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

A carrier protein strategy yields the structure of dalbavancin.

Economou, N.J.Nahoum, V.Weeks, S.D.Grasty, K.C.Zentner, I.J.Townsend, T.M.Bhuiya, M.W.Cocklin, S.Loll, P.J.

(2012) J Am Chem Soc 134: 4637-4645

  • DOI: 10.1021/ja208755j
  • Primary Citation of Related Structures:  
    3RUL, 3RUM, 3RUN

  • PubMed Abstract: 
  • Many large natural product antibiotics act by specifically binding and sequestering target molecules found on bacterial cells. We have developed a new strategy to expedite the structural analysis of such antibiotic-target complexes, in which we covalently link the target molecules to carrier proteins, and then crystallize the entire carrier-target-antibiotic complex ...

    Many large natural product antibiotics act by specifically binding and sequestering target molecules found on bacterial cells. We have developed a new strategy to expedite the structural analysis of such antibiotic-target complexes, in which we covalently link the target molecules to carrier proteins, and then crystallize the entire carrier-target-antibiotic complex. Using native chemical ligation, we have linked the Lys-D-Ala-D-Ala binding epitope for glycopeptide antibiotics to three different carrier proteins. We show that recognition of this peptide by multiple antibiotics is not compromised by the presence of the carrier protein partner, and use this approach to determine the first-ever crystal structure for the new therapeutic dalbavancin. We also report the first crystal structure of an asymmetric ristocetin antibiotic dimer, as well as the structure of vancomycin bound to a carrier-target fusion. The dalbavancin structure reveals an antibiotic molecule that has closed around its binding partner; it also suggests mechanisms by which the drug can enhance its half-life by binding to serum proteins, and be targeted to bacterial membranes. Notably, the carrier protein approach is not limited to peptide ligands such as Lys-D-Ala-D-Ala, but is applicable to a diverse range of targets. This strategy is likely to yield structural insights that accelerate new therapeutic development.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Maltose-binding periplasmic proteinA378Escherichia coli K-12Mutation(s): 0 
Gene Names: malEb4034JW3994
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RistocetinB, C7Amycolatopsis luridaMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-arabinofuranose-(1-2)-alpha-D-mannopyranose-(1-2)-[alpha-L-rhamnopyranose-(1-6)]beta-D-glucopyranoseD, E4N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G77120YG
GlyCosmos:  G77120YG
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseF2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN (Subject of Investigation/LOI)
Query on MAN

Download Ideal Coordinates CCD File 
N [auth B], P [auth C]alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
RST
Query on RST

Download Ideal Coordinates CCD File 
M [auth B], O [auth C]3-amino-2,3,6-trideoxy-alpha-L-ribo-hexopyranose
C6 H13 N O3
BBMKQGIZNKEDOX-KCDKBNATSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
J [auth A], K [auth A], L [auth A], Q [auth C]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
IPA
Query on IPA

Download Ideal Coordinates CCD File 
G [auth A], H [auth A], I [auth A]ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
CCS
Query on CCS
AL-PEPTIDE LINKINGC5 H9 N O4 SCYS
MDF
Query on MDF
B, CL-PEPTIDE LINKINGC9 H11 N O4TYR
OMX
Query on OMX
B, CL-PEPTIDE LINKINGC9 H11 N O4TYR
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 4
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900001
Query on PRD_900001
Falpha-maltoseOligosaccharide / Nutrient Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.833α = 90
b = 75.005β = 90
c = 90.778γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-06
    Type: Initial release
  • Version 1.1: 2016-02-17
    Changes: Derived calculations, Non-polymer description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Structure summary