8C4Q | pdb_00008c4q

CdaA-Apo

• PDB DOI: https://doi.org/10.2210/pdb8C4Q/pdb

• Classification: PROTEIN BINDING
• Organism(s): Listeria monocytogenes
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-01-04 Released: 2023-06-07 
• Deposition Author(s): Neumann, P., Ficner, R.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.217 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.190 (Depositor) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Computer-aided design of a cyclic di-AMP synthesizing enzyme CdaA inhibitor.

Neumann, P., Kloskowski, P., Ficner, R.

(2023) Microlife 4: uqad021-uqad021

• PubMed: 37223749 
• DOI: https://doi.org/10.1093/femsml/uqad021
• Primary Citation Related Structures: 
  8C4J, 8C4M, 8C4N, 8C4O, 8C4P, 8C4Q, 8C4R


• PubMed Abstract: 
  

  Cyclic di-AMP (c-di-AMP) is an essential secondary messenger regulating cell wall homeostasis and myriads of physiological processes in several Gram-positive and mycobacteria, including human pathogens. Hence, c-di-AMP synthesizing enzymes (DACs) have become a promising antibacterial drug target. To overcome a scarcity of small molecule inhibitors of c-di-AMP synthesizing enzyme CdaA, a computer-aided design of a new compound that should block the enzyme has been performed. This has led to the identification of a molecule comprising two thiazole rings and showing inhibitory potential based on ITC measurements. Thiazole scaffold is a good pharmacophore nucleus known due to its various pharmaceutical applications. It is contained in more than 18 FDA-approved drugs as well as in dozens of experimental drugs. Hence, the designed inhibitor can serve as a potent lead compound for further development of inhibitor against CdaA.

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Organizational Affiliation: 
• Department of Molecular Structural Biology, Georg-August-University Goettingen, Institute of Microbiology and Genetics, GZMB, Justus-von-Liebig Weg 11, 37077 Goettingen, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 38.92 kDa 
• Atom Count: 2,718 
• Modeled Residue Count: 317 
• Deposited Residue Count: 356 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diadenylate cyclase	A, B	178	Listeria monocytogenes	Mutation(s): 0  Gene Names: dacA, cdaA, lmo2120 EC: 2.7.7.85
UniProt
Find proteins for Q8Y5E4 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y5E4  Go to UniProtKB:  Q8Y5E4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth B], E [auth B], F [auth B], G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.217 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.190 (Depositor) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.7	α = 90
b = 64.52	β = 90
c = 129.48	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-06-07 
Deposition Author(s): Neumann, P., Ficner, R.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SPP1879
German Research Foundation (DFG)	Germany	SFB860

Revision History  

• Version 1.0: 2023-06-07
  Type: Initial release
  
• Version 1.1: 2024-06-19
  Changes: Data collection, Database references