4KQV

Topoisomerase iv atp binding domain of francisella tularensis in complex with a small molecule inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.257 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted DOOClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Topoisomerase IV, subunit B
A, B
390Francisella tularensis subsp. holarctica LVSMutation(s): 1 
Gene Names: DNA TOPOISOMERASE IV SUBUNIT B PAREFTL_1726
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for A0A0J9WZF0 (Francisella tularensis subsp. holarctica (strain LVS))
Explore A0A0J9WZF0 
Go to UniProtKB:  A0A0J9WZF0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0J9WZF0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DOO
Query on DOO

Download Ideal Coordinates CCD File 
E [auth A],
L [auth B]
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
IOD
Query on IOD

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
F [auth A]
G [auth A]
H [auth A]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.257 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.2α = 90
b = 163.16β = 91.81
c = 72.28γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted DOOClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-15
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Structure summary
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description