4KFG

The DNA Gyrase B ATP binding domain of Escherichia coli in complex with a small molecule inhibitor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 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
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase subunit BA, B215Escherichia coli K-12Mutation(s): 0 
Gene Names: acrBhimBhisUnalCparApcbAgyrBcoub3699JW5625
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for P0AES6 (Escherichia coli (strain K12))
Explore P0AES6 
Go to UniProtKB:  P0AES6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AES6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DOO
Query on DOO

Download Ideal Coordinates CCD File 
E [auth A],
G [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
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
F [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
DOO BindingDB:  4KFG Ki: 0.05 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.894α = 90
b = 82.477β = 100.16
c = 53.74γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-15
    Type: Initial release