3D1G

Structure of a small molecule inhibitor bound to a DNA sliding clamp


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.256 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of a small-molecule inhibitor of a DNA polymerase sliding clamp.

Georgescu, R.E.Yurieva, O.Kim, S.S.Kuriyan, J.Kong, X.P.O'Donnell, M.

(2008) Proc.Natl.Acad.Sci.Usa 105: 11116-11121

  • DOI: 10.1073/pnas.0804754105
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • DNA polymerases attach to the DNA sliding clamp through a common overlapping binding site. We identify a small-molecule compound that binds the protein-binding site in the Escherichia coli beta-clamp and differentially affects the activity of DNA pol ...

    DNA polymerases attach to the DNA sliding clamp through a common overlapping binding site. We identify a small-molecule compound that binds the protein-binding site in the Escherichia coli beta-clamp and differentially affects the activity of DNA polymerases II, III, and IV. To understand the molecular basis of this discrimination, the cocrystal structure of the chemical inhibitor is solved in complex with beta and is compared with the structures of Pol II, Pol III, and Pol IV peptides bound to beta. The analysis reveals that the small molecule localizes in a region of the clamp to which the DNA polymerases attach in different ways. The results suggest that the small molecule may be useful in the future to probe polymerase function with beta, and that the beta-clamp may represent an antibiotic target.


    Organizational Affiliation

    The Rockefeller University and Howard Hughes Medical Institute, 1230 York Avenue, P. O. Box 228, New York, NY 10065, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase III subunit beta
A, B
366Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: dnaN
Find proteins for P0A988 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A988
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
322
Query on 322

Download SDF File 
Download CCD File 
A, B
[(5R)-5-(2,3-dibromo-5-ethoxy-4-hydroxybenzyl)-4-oxo-2-thioxo-1,3-thiazolidin-3-yl]acetic acid
C14 H13 Br2 N O5 S2
ABQHPGHMYXJJIV-MRVPVSSYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
322Ki: ~10000 nM BINDINGMOAD
322Ki: 10000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.256 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 35.720α = 110.24
b = 79.395β = 100.58
c = 80.505γ = 99.46
Software Package:
Software NamePurpose
ADSCdata collection
CNSrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
CNSphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description
  • Version 1.3: 2018-01-24
    Type: Structure summary