3RUL

New strategy to analyze structures of glycopeptide-target complexes

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.0 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:  

  • 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 coval ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
A, B, C, D
79Homo sapiensMutation(s): 0 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Go to Gene View: UBC
Go to UniProtKB:  P0CG48
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Dalbavancin
E, F, G, H
7N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL
Download SDF File 
Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MAN
Query on MAN
Download SDF File 
Download CCD File 
E, F, G, H
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
TLA
Query on TLA
Download SDF File 
Download CCD File 
A, B
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
M12
Query on M12
Download SDF File 
Download CCD File 
E, F, G, H
10-METHYLUNDECANOIC ACID
C12 H24 O2
QJRRBVNPIKYRQJ-UHFFFAOYSA-N
 Ligand Interaction
N1L
Query on N1L
Download SDF File 
Download CCD File 
E, F, G, H
2-AMINO-2-DEOXY-BETA-D-GLUCOPYRANURONIC ACID
C6 H11 N O6
CRIPFXSBMSGPKB-LVBGKUAWSA-N
 Ligand Interaction
Modified Residues  8 Unique
IDChainsTypeFormula2D DiagramParent
CCS
Query on CCS
A, B, C, D
L-PEPTIDE LINKINGC5 H9 N O4 SCYS
HG7
Query on HG7
E, F, G, H
L-peptide linkingC13 H21 N3 O2

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DAL
Query on DAL
A, B, C, D
D-PEPTIDE LINKINGC3 H7 N O2

--

GHP
Query on GHP
E, F, G, H
D-PEPTIDE LINKINGC8 H9 N O3

--

HCL
Query on HCL
E, F, G, H
L-peptide linkingC8 H8 Cl N O4

--

HGM
Query on HGM
E, F, G, H
D-peptide linkingC9 H11 N O3

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OMY
Query on OMY
E, F, G, H
L-PEPTIDE LINKINGC9 H10 Cl N O4TYR
DTY
Query on DTY
E, F, G, H
D-PEPTIDE LINKINGC9 H11 N O3

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.243 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.300α = 90.00
b = 86.250β = 90.00
c = 107.190γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-06-06
    Type: Initial release