6TZV

Crystal Structure of the carboxyltransferase subunit of ACC (AccD6) in complex with inhibitor Phenyl-Cyclodiaone from Mycobacterium tuberculosis

• PDB DOI: https://doi.org/10.2210/pdb6TZV/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-08-13 Released: 2020-08-19 
• Deposition Author(s): Reddy, M.C.M., Zhou, N., Sacchettini, J., TB Structural Genomics Consortium (TBSGC)
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 0.204 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 

Literature

Novel herbicidal derivatives that inhibit carboxyltransferase subunit of the acetyl-CoA carboxylase in Mycobacterium tuberculosis

Reddy, M.C.M., Zhou, N., Sacchettini, J.

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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 404.79 kDa 
• Atom Count: 26,029 
• Modelled Residue Count: 3,375 
• Deposited Residue Count: 3,784 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable propionyl-CoA carboxylase beta chain 6	A, B, C, D, E, F, G, H	473	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: accD6, Rv2247, MTCY427.28 EC: 6.4.1.3
UniProt
Find proteins for P9WQH5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WQH5  Go to UniProtKB:  P9WQH5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PKP (Subject of Investigation/LOI)	I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	4'-[(6-chloro-1,3-benzothiazol-2-yl)oxy]-6-hydroxy-4,4-dimethyl-4,5-dihydro[1,1'-biphenyl]-2(3H)-one C21 H18 Cl N O3 S POUJNUFBEAPAJW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 0.204 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.345	α = 90
b = 153.069	β = 90.08
c = 150.184	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-08-19 
Deposition Author(s): Reddy, M.C.M., Zhou, N., Sacchettini, J., TB Structural Genomics Consortium (TBSGC)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	--

Revision History  

• Version 1.0: 2020-08-19
  Type: Initial release
  
• Version 1.1: 2024-03-13
  Changes: Data collection, Database references