4K4O

The DNA Gyrase B ATP binding domain of Enterococcus faecalis in complex with a small molecule inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4K4O/pdb

• Classification: ISOMERASE/ISOMERASE INHIBITOR
• Organism(s): Enterococcus faecalis V583
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-04-12 Released: 2014-01-15 
• Deposition Author(s): Bensen, D.C., Akers-Rodriguez, S., Lam, T., Tari, L.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.196 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 

Literature

A new class of type IIA topoisomerase inhibitors with broad-spectrum antibacterial activity

Tari, L.W., Bensen, D.C., Finn, J.

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: 24.34 kDa 
• Atom Count: 1,802 
• Modelled Residue Count: 190 
• Deposited Residue Count: 215 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit B	A	215	Enterococcus faecalis V583	Mutation(s): 0  Gene Names: EF_0005, gyrB EC: 5.99.1.3
UniProt
Find proteins for Q839Z1 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q839Z1  Go to UniProtKB:  Q839Z1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DOO	B [auth A]	6-fluoro-4-[(3aR,6aR)-hexahydropyrrolo[3,4-b]pyrrol-5(1H)-yl]-N-methyl-2-[(2-methylpyrimidin-5-yl)oxy]-9H-pyrimido[4,5-b]indol-8-amine C22 H23 F N8 O ACMIJDVJWLMBCX-PXAZEXFGSA-N
TBU	C [auth A]	TERTIARY-BUTYL ALCOHOL C4 H10 O DKGAVHZHDRPRBM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.196 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.45	α = 90
b = 58.35	β = 90
c = 65.55	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-15 
Deposition Author(s): Bensen, D.C., Akers-Rodriguez, S., Lam, T., Tari, L.W.

Revision History  

• Version 1.0: 2014-01-15
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description