4KSH

Dna gyrase atp binding domain of enterococcus faecalis in complex with a small molecule inhibitor (7-({4-[(3R)-3-AMINOPYRROLIDIN-1-YL]-5-CHLORO-6-ETHYL-7H-PYRROLO[2,3-D]PYRIMIDIN-2-YL}SULFANYL)-1,5-NAPHTHYRIDIN-1(4H)-OL)

• PDB DOI: https://doi.org/10.2210/pdb4KSH/pdb

• Classification: Isomerase/isomerase inhibitor
• Organism(s): Enterococcus faecalis V583
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-05-17 Released: 2014-01-15 
• Deposition Author(s): Bensen, D.C., Akers-Rodriguez, S., Tari, L.W.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.205 
• R-Value Work: 0.171 
• R-Value Observed: 0.173 

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: 24.37 kDa 
• Atom Count: 1,795 
• Modelled Residue Count: 193 
• 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 (PDB Primary Data), 5.6.2.2 (UniProt)
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
HTT	B [auth A]	7-({4-[(3R)-3-aminopyrrolidin-1-yl]-5-chloro-6-ethyl-7H-pyrrolo[2,3-d]pyrimidin-2-yl}sulfanyl)-1,5-naphthyridin-1(4H)-ol C20 H22 Cl N7 O S GAOGTYTXXMCXHI-LLVKDONJSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.205 
• R-Value Work: 0.171 
• R-Value Observed: 0.173 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.83	α = 90
b = 58.34	β = 90
c = 65.88	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., Tari, L.W.

Revision History  

• Version 1.0: 2014-01-15
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations