4UCO | pdb_00004uco

Fragment bound to H.influenza NAD dependent DNA ligase

• PDB DOI: https://doi.org/10.2210/pdb4UCO/pdb

• Classification: LIGASE
• Organism(s): Haemophilus influenzae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-12-04 Released: 2015-10-14 
• Deposition Author(s): Hale, M., Brassington, C., Carcanague, D., Embrey, K., Eyermann, C.J., Giacobbe, R.A., Gingipali, L., Gowravaram, M., Harang, J., Howard, T., Ioannidis, G., Jahic, H., Kutschke, A., Laganas, V.A., Loch, J., Miller, M.D., Murphy-Benenato, K.E., Oguto, H., Otterbein, L., Patel, S.J., Shapiro, A.B., Boriack-Sjodin, P.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.254 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.220 (Depositor) 
• R-Value Observed: 
  0.222 (Depositor) 

Literature

From Fragments to Leads: Novel Bacterial Nad+-Dependent DNA Ligase Inhibitors

Hale, M., Brassington, C., Carcanague, D., Embrey, K., Eyermann, C.J., Giacobbe, R.A., Gingipali, L., Gowravaram, M., Harang, J., Howard, T., Ioannidis, G., Jahic, H., Kutschke, A., Laganas, V.A., Loch, J., Miller, M.D., Murphy-Benenato, K.E., Oguto, H., Otterbein, L., Patel, S.J., Shapiro, A.B., Boriack-Sjodin, P.A.

(2015) Tetrahedron Lett 56: 3108

• DOI: https://doi.org/10.1016/J.TETLET.2014.12.067

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: 37.08 kDa 
• Atom Count: 2,600 
• Modeled Residue Count: 317 
• Deposited Residue Count: 324 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA LIGASE	A	324	Haemophilus influenzae	Mutation(s): 0  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
D41	B [auth A]	7-amino-2-tert-butyl-4-(1H-pyrrol-2-yl)pyrido[2,3-d]pyrimidine-6-carboxamide C16 H18 N6 O QZUNGZQACLCXSW-UHFFFAOYSA-N
IWH	C [auth A]	1-(2,4-dimethylbenzyl)-6-oxo-1,6-dihydropyridine-3-carboxamide C15 H16 N2 O2 TUJVPUNUHQIBSM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.254 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.220 (Depositor) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.008	α = 90
b = 137.008	β = 90
c = 55.974	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-14 
Deposition Author(s): Hale, M., Brassington, C., Carcanague, D., Embrey, K., Eyermann, C.J., Giacobbe, R.A., Gingipali, L., Gowravaram, M., Harang, J., Howard, T., Ioannidis, G., Jahic, H., Kutschke, A., Laganas, V.A., Loch, J., Miller, M.D., Murphy-Benenato, K.E., Oguto, H., Otterbein, L., Patel, S.J., Shapiro, A.B., Boriack-Sjodin, P.A.

Revision History  

• Version 1.0: 2015-10-14
  Type: Initial release
  
• Version 1.1: 2018-04-04
  Changes: Data collection
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other