3VFK

The structure of monodechloro-teicoplanin in complex with its ligand, using ubiquitin as a ligand carrier


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.278 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of the complex between teicoplanin and a bacterial cell-wall peptide: use of a carrier-protein approach.

Economou, N.J.Zentner, I.J.Lazo, E.Jakoncic, J.Stojanoff, V.Weeks, S.D.Grasty, K.C.Cocklin, S.Loll, P.J.

(2013) Acta Crystallogr.,Sect.D 69: 520-533

  • DOI: 10.1107/S0907444912050469
  • Primary Citation of Related Structures:  3VFJ

  • PubMed Abstract: 
  • Multidrug-resistant bacterial infections are commonly treated with glycopeptide antibiotics such as teicoplanin. This drug inhibits bacterial cell-wall biosynthesis by binding and sequestering a cell-wall precursor: a D-alanine-containing peptide. A ...

    Multidrug-resistant bacterial infections are commonly treated with glycopeptide antibiotics such as teicoplanin. This drug inhibits bacterial cell-wall biosynthesis by binding and sequestering a cell-wall precursor: a D-alanine-containing peptide. A carrier-protein strategy was used to crystallize the complex of teicoplanin and its target peptide by fusing the cell-wall peptide to either MBP or ubiquitin via native chemical ligation and subsequently crystallizing the protein-peptide-antibiotic complex. The 2.05 Å resolution MBP-peptide-teicoplanin structure shows that teicoplanin recognizes its ligand through a combination of five hydrogen bonds and multiple van der Waals interactions. Comparison of this teicoplanin structure with that of unliganded teicoplanin reveals a flexibility in the antibiotic peptide backbone that has significant implications for ligand recognition. Diffraction experiments revealed an X-ray-induced dechlorination of the sixth amino acid of the antibiotic; it is shown that teicoplanin is significantly more radiation-sensitive than other similar antibiotics and that ligand binding increases radiosensitivity. Insights derived from this new teicoplanin structure may contribute to the development of next-generation antibacterials designed to overcome bacterial resistance.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ubiquitin, C-terminal fused by Cys-Lys-D-Ala-D-Ala
A
79Homo sapiensGene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Go to Gene View: UBC
Go to UniProtKB:  P0CG48
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MonodeChloro- Teicoplanin A2-2
G
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
GCS
Query on GCS

Download SDF File 
Download CCD File 
G
D-GLUCOSAMINE
2-AMINO-2-DEOXY-D-GLUCOSE
C6 H13 N O5
MSWZFWKMSRAUBD-QZABAPFNSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
G
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
G
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
T55
Query on T55

Download SDF File 
Download CCD File 
G
8-METHYLNONANOIC ACID
C10 H20 O2
OAOABCKPVCUNKO-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000882
Query on PRD_000882
GMonodeChloro- Teicoplanin A2-2Glycopeptide / Antibiotic

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Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CCS
Query on CCS
A
L-PEPTIDE LINKINGC5 H9 N O4 SCYS
DAL
Query on DAL
A
D-PEPTIDE LINKINGC3 H7 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.278 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 88.010α = 90.00
b = 25.180β = 109.18
c = 38.710γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
MOLREPphasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-09
    Type: Initial release
  • Version 1.1: 2013-03-27
    Type: Structure summary
  • Version 1.2: 2013-04-03
    Type: Derived calculations
  • Version 1.3: 2013-06-19
    Type: Database references