9FOY

Ternary complex of a Mycobacterium tuberculosis DNA gyrase core fusion with DNA and the inhibitor AMK32b

• PDB DOI: https://doi.org/10.2210/pdb9FOY/pdb
• NAKB: 9FOY

• Classification: ISOMERASE
• Organism(s): Mycobacterium tuberculosis H37Rv, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-06-12 Released: 2024-08-07 
• Deposition Author(s): Kokot, M., Hrast, M., Feng, L., Mitchenall, L.A., Lawson, D.M., Maxwell, A., Minovski, N., Anderluh, M.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.304 
• R-Value Work: 0.279 
• R-Value Observed: 0.281 

Starting Model: experimental

Literature

Unraveling the Mycobacterium tuberculosis DNA gyrase-DNA-NBTI complex

Kokot, M., Hrast, M., Feng, L., Mitchenall, L.A., Lawson, D.M., Maxwell, A., Minovski, N., Anderluh, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 181.96 kDa 
• Atom Count: 12,316 
• Modelled Residue Count: 1,500 
• Deposited Residue Count: 1,552 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit B,DNA gyrase subunit A	A, B	756	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: gyrB, Rv0005, MTCY10H4.03, gyrA, Rv0006, MTCY10H4.04 EC: 5.6.2.2
UniProt
Find proteins for P9WG47 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WG47  Go to UniProtKB:  P9WG47
Find proteins for P9WG45 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WG45  Go to UniProtKB:  P9WG45
UniProt Groups	P9WG45P9WG47

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*G)-3')	C [auth E], E [auth G]	8	Mycobacterium tuberculosis H37Rv

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')	D [auth F], F [auth H]	12	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1ID9 (Subject of Investigation/LOI)	H	(1~{R})-2-[4-[[4-bromanyl-3,5-bis(fluoranyl)phenyl]methylamino]cyclohexyl]-1-(6-methoxy-1,5-naphthyridin-4-yl)ethanol C24 H26 Br F2 N3 O2 RCLQISQKEHCDJQ-IUSZMWJPSA-N
A1ID8 (Subject of Investigation/LOI)	G [auth H]	(1~{S})-2-[4-[[4-bromanyl-3,5-bis(fluoranyl)phenyl]methylamino]cyclohexyl]-1-(6-methoxy-1,5-naphthyridin-4-yl)ethanol C24 H26 Br F2 N3 O2 RCLQISQKEHCDJQ-HTZUNMPGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.304 
• R-Value Work: 0.279 
• R-Value Observed: 0.281 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.041	α = 90
b = 131.703	β = 97.23
c = 96.281	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
DIALS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-07 
Deposition Author(s): Kokot, M., Hrast, M., Feng, L., Mitchenall, L.A., Lawson, D.M., Maxwell, A., Minovski, N., Anderluh, M.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/P012523/1
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/V006983/1

Revision History  

• Version 1.0: 2024-08-07
  Type: Initial release