6Y8O

Mycobacterium smegmatis GyrB 22kDa ATPase sub-domain in complex with novobiocin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.137 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural and mechanistic analysis of ATPase inhibitors targeting mycobacterial DNA gyrase.

Henderson, S.R.Stevenson, C.E.M.Malone, B.Zholnerovych, Y.Mitchenall, L.A.Pichowicz, M.McGarry, D.H.Cooper, I.R.Charrier, C.Salisbury, A.M.Lawson, D.M.Maxwell, A.

(2020) J Antimicrob Chemother 75: 2835-2842

  • DOI: 10.1093/jac/dkaa286
  • Primary Citation of Related Structures:  
    6Y8N, 6Y8O, 6Y8L

  • PubMed Abstract: 
  • To evaluate the efficacy of two novel compounds against mycobacteria and determine the molecular basis of their action on DNA gyrase using structural and mechanistic approaches.


    Organizational Affiliation

    Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase subunit BA, B234Mycolicibacterium smegmatisMutation(s): 2 
Gene Names: gyrB
EC: 5.6.2.2
UniProt
Find proteins for A0QNE0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QNE0 
Go to UniProtKB:  A0QNE0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NOV (Subject of Investigation/LOI)
Query on NOV

Download Ideal Coordinates CCD File 
C [auth A], M [auth B]NOVOBIOCIN
C31 H36 N2 O11
YJQPYGGHQPGBLI-KGSXXDOSSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A] , E [auth A] , F [auth A] , G [auth A] , H [auth A] , N [auth B] , O [auth B] , P [auth B] , 
D [auth A],  E [auth A],  F [auth A],  G [auth A],  H [auth A],  N [auth B],  O [auth B],  P [auth B],  Q [auth B],  R [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
I [auth A], J [auth A], S [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
K [auth A], L [auth A], T [auth B], U [auth B], V [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.137 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.962α = 90
b = 56.112β = 90.66
c = 50.678γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/P012523/1
Wellcome TrustUnited Kingdom110072/Z/15/Z

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-12
    Type: Initial release
  • Version 1.1: 2020-09-30
    Changes: Database references