Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 82259.41 
• Atom Count: 5736 
• Residue Count: 732 
• Unique protein chains: 1

3D1G

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

• DOI: 10.2210/pdb3D1G/pdb

• Classification: TRANSFERASE TRANSCRIPTION
• Organism(s): Escherichia coli (strain K12)
• Expression System: Escherichia coli


• Deposited: 2008-05-05 Released: 2008-07-29 
• Deposition Author(s): Georgescu, R.E., Yurieva, O., Seung-Sup, K., Kuriyan, J., Kong, X.-P., O'Donnell, M.

---

Experimental Data Snapshot

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

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

• PubMed: 18678908 
• DOI: 10.1073/pnas.0804754105
• Primary Citation of Related Structures:  
  3D1F, 3D1E


• 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 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
Molecule	Chains	Sequence Length	Organism	Details
DNA polymerase III subunit beta	A, B	366	Escherichia 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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
322	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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
322	Ki: ~10000 nM BINDINGMOAD
322	Ki: 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 = 35.720	α = 110.24
b = 79.395	β = 100.58
c = 80.505	γ = 99.46

Software Package:

Software Name	Purpose
ADSC	data collection
CNS	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
CNS	phasing
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-05-05 
• Released Date: 2008-07-29 
• Deposition Author(s): Georgescu, R.E., Yurieva, O., Seung-Sup, K., Kuriyan, J., Kong, X.-P., O'Donnell, M.

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