4EEQ

Crystal structure of E. faecalis DNA ligase with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4EEQ/pdb

• Classification: Ligase/Ligase inhibitor
• Organism(s): Enterococcus faecalis
• Mutation(s): No 


• Deposited: 2012-03-28 Released: 2013-04-03 
• Deposition Author(s): Wang, T., Charifson, P., Wei, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.245 
• R-Value Work: 0.184 
• R-Value Observed: 0.192 

Literature

Design, Synthesis and Activity Evaluation of Potent NAD+ DNA Ligase Inhibitors as Potential Antibacterial Agents.

Wang, T., Charifson, P., Wei, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 38.68 kDa 
• Atom Count: 3,001 
• Modelled Residue Count: 313 
• Deposited Residue Count: 331 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA ligase	A	331	Enterococcus faecalis	Mutation(s): 0  Gene Names: ligA, EF_0722 EC: 6.5.1.2
UniProt
Find proteins for Q837V6 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q837V6  Go to UniProtKB:  Q837V6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NMN	D [auth A]	BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE C11 H16 N2 O8 P DAYLJWODMCOQEW-TURQNECASA-O
0OX	E [auth A]	4-amino-2-(cyclopentyloxy)pyrimidine-5-carboxamide C10 H14 N4 O2 YTVJKSRJMDSHEP-UHFFFAOYSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.245 
• R-Value Work: 0.184 
• R-Value Observed: 0.192 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.38	α = 90
b = 86.46	β = 101.05
c = 57	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
CNX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-03 
Deposition Author(s): Wang, T., Charifson, P., Wei, Y.

Revision History  

• Version 1.0: 2013-04-03
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations