Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

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: 82.26 kDa 
• Atom Count: 6533 
• Modelled Residue Count: 732 
• Deposited 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
• Expression System: Escherichia coli
• Mutation(s): No 


• 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.

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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 U S A 105: 11116-11121

• PubMed: 18678908 
• DOI: 10.1073/pnas.0804754105
• Primary Citation of Related Structures:  
  3D1E, 3D1F, 3D1G


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase III subunit beta	A, B	366	Escherichia coli	Mutation(s): 0  Gene Names: dnaN EC: 2.7.7.7
UniProt
Find proteins for P0A988 (Escherichia coli (strain K12)) Explore P0A988  Go to UniProtKB:  P0A988

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
322 (Subject of Investigation/LOI)	C [auth A], D [auth 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

Binding Affinity Annotations
ID	Source	Binding Affinity
322	PDBBind:  3D1G	Ki: 1.00e+4 (nM) from 1 assay(s)
	Binding MOAD:  3D1G	Ki: 1.00e+4 (nM) from 1 assay(s)

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 = 35.72	α = 110.24
b = 79.395	β = 100.58
c = 80.505	γ = 99.46

Software Package:

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

Structure Validation

Ligand Structure Quality Assessment  

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
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2018-01-24
  Changes: Structure summary