3BAC | pdb_00003bac

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

• PDB DOI: https://doi.org/10.2210/pdb3BAC/pdb

• Classification: LIGASE
• Organism(s): Haemophilus influenzae
• 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: 3.00 Å
• R-Value Free: 
  0.265 (Depositor) 
• R-Value Work: 
  0.216 (Depositor) 

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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 30.86 kDa 
• Atom Count: 2,060 
• Modeled Residue Count: 255 
• Deposited Residue Count: 270 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA ligase	A	270	Haemophilus influenzae	Mutation(s): 0  Gene Names: ligN, lig EC: 6.5.1.2
UniProt
Find proteins for P43813 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Explore P43813  Go to UniProtKB:  P43813

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3B9	E [auth A]	N-[2-(2,4-diaminopyrido[2,3-d]pyrimidin-7-yl)-2-methylpropyl]-4-phenoxybenzamide C24 H24 N6 O2 FDJWFDQRPKKBFA-UHFFFAOYSA-N
PO4	B [auth A], C [auth A], D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.265 (Depositor) 
• R-Value Work:  0.216 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.031	α = 90
b = 95.031	β = 90
c = 197.183	γ = 120

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