3RUM

New strategy to analyze structures of glycopeptide antibiotic-target complexes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.851 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.1 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
Maltose-binding periplasmic protein
A
378Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: malE
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AEX9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ristocetin
B, C
7N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAL
Query on MAL

Download SDF File 
Download CCD File 
A
MALTOSE
C12 H22 O11
GUBGYTABKSRVRQ-ASMJPISFSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
RAM
Query on RAM

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Download CCD File 
B, C
ALPHA-L-RHAMNOSE
C6 H12 O5
SHZGCJCMOBCMKK-HGVZOGFYSA-N
 Ligand Interaction
BXY
Query on BXY

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Download CCD File 
B, C
alpha-D-arabinofuranose
C5 H10 O5
HMFHBZSHGGEWLO-MBMOQRBOSA-N
 Ligand Interaction
MAN
Query on MAN

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Download CCD File 
B, C
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BGC
Query on BGC

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

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Download CCD File 
B, C
RISTOSAMINE
C6 H13 N O3
BBMKQGIZNKEDOX-KCDKBNATSA-N
 Ligand Interaction
IPA
Query on IPA

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Download CCD File 
A
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  7 Unique
IDChainsTypeFormula2D DiagramParent
CCS
Query on CCS
A
L-PEPTIDE LINKINGC5 H9 N O4 SCYS
OMX
Query on OMX
B, C
L-PEPTIDE LINKINGC9 H11 N O4TYR
HTY
Query on HTY
B, C
D-peptide linkingC9 H11 N O4

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MDF
Query on MDF
B, C
L-PEPTIDE LINKINGC9 H11 N O4TYR
MP4
Query on MP4
B, C
L-peptide linkingC9 H11 N O4

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DAL
Query on DAL
A
D-PEPTIDE LINKINGC3 H7 N O2

--

GHP
Query on GHP
B, C
D-PEPTIDE LINKINGC8 H9 N O3

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.851 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.833α = 90.00
b = 75.005β = 90.00
c = 90.778γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-06-06
    Type: Initial release
  • Version 1.1: 2016-02-17
    Type: Derived calculations, Non-polymer description