3BA9

Structural Basis for Inhbition of NAD-Dependent Ligase

• PDB DOI: https://doi.org/10.2210/pdb3BA9/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: 0.216 
• R-Value Work: 0.184 

Literature

Structural Basis for Inhbition of NAD-Dependent 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: 39.46 kDa 
• Atom Count: 2,899 
• 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3B9	G [auth A]	N-[2-(2,4-diaminopyrido[2,3-d]pyrimidin-7-yl)-2-methylpropyl]-4-phenoxybenzamide C24 H24 N6 O2 FDJWFDQRPKKBFA-UHFFFAOYSA-N
NMN	F [auth A]	BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE C11 H16 N2 O8 P DAYLJWODMCOQEW-TURQNECASA-O
SO4	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	H [auth A], I [auth A], J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.216 
• R-Value Work: 0.184 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.248	α = 90
b = 86.277	β = 101.11
c = 57.143	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
CNX	refinement

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: Non-polymer description, Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations