3BA8

Structural Basis for the Inhibition of Bacterial NAD+ Dependent DNA Ligase

• PDB DOI: https://doi.org/10.2210/pdb3BA8/pdb

• Classification: LIGASE
• Organism(s): Enterococcus faecalis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-11-07 Released: 2008-11-11 
• Deposition Author(s): Pinko, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.223 
• R-Value Work: 0.193 

Literature

Structural Basis for the Inhibition of Bacterial NAD+ Dependent DNA Ligase

Pinko, C., Borchardt, A., Nikulin, V., Su, 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: 38.93 kDa 
• Atom Count: 2,854 
• Modelled Residue Count: 313 
• Deposited Residue Count: 332 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA ligase	A	332	Enterococcus faecalis	Mutation(s): 0  Gene Names: ligA 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	E [auth A]	BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE C11 H16 N2 O8 P DAYLJWODMCOQEW-TURQNECASA-O
3B8	F [auth A]	2-amino-7-fluoro-5-oxo-5H-chromeno[2,3-b]pyridine-3-carboxamide C13 H8 F N3 O3 GCHMLYYPYFXLQB-UHFFFAOYSA-N
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.223 
• R-Value Work: 0.193 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.496	α = 90
b = 86.285	β = 100.939
c = 56.609	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-11 
Deposition Author(s): Pinko, C.

Revision History  

• Version 1.0: 2008-11-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations