9TXD | pdb_00009txd

N-terminal domain of ClpC from S. aureus

• PDB DOI: https://doi.org/10.2210/pdb9TXD/pdb

• Classification: CHAPERONE
• Organism(s): Staphylococcus aureus subsp. aureus NCTC 8325
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2026-01-15 Released: 2026-09-16 
• Deposition Author(s): Kopp, J., Schwan, M., Sinning, I.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.215 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: in silico

Literature

Small-molecule activators of the Staphylococcus aureus ClpC/ClpP AAA+ protease.

Jenne, T., Viliuga, V., Uhrig, U., Jehle, B., Schwan, M., Kopp, J., Flemming, D., Seebach, E., Sinning, I., Bukau, B., Mogk, A.

(2026) iScience 29: 117738-117738

• PubMed: 42866717 
• DOI: https://doi.org/10.1016/j.isci.2026.117738
• Primary Citation Related Structures: 
  9TXC, 9TXD


• PubMed Abstract: 
  

  The central AAA+ ClpC/ClpP protease in Gram-positive bacteria is crucial for virulence and stress resistance and has been recognized as drug target. Natural cyclic peptides deregulate the essential Mycobacterium tuberculosis ClpC1 and cause cell death. Similarly, overactivated mutants of the non-essential Staphylococcus aureus ClpC homolog cause uncontrolled proteolysis and severe toxicity in vivo . However, no chemical modulators of S. aureus ClpC have been described. Here, using a biochemical high-throughput screen, we identify eight distinct bona fide small molecules that stimulate ClpC ATPase and proteolytic activity in vitro . Structural, computational, and mutational analyses define two ligandable regulatory sites within the ClpC N-terminal domain (NTD) as compound targets: a conserved hydrophobic groove and an allosteric pArg1 pocket, both engaged in substrate recognition. These findings establish S. aureus ClpC as chemically targetable and provide mechanistic insight into its regulatory architecture, enabling future development and optimization of chemical probes to deregulate AAA+ protease control.

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Organizational Affiliation: 
• Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany.
Department of Biochemistry and Biophysics at Stockholm University and Science for Life Laboratory, Stockholm, Sweden.
The European Molecular Biology Laboratory, EMBL, Meyerhofstraße 1, 69120 Heidelberg, Germany.
Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany.
Department of Infectious Diseases, Medical Microbiology and Hygiene, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany.
University Hospital Heidelberg, Heidelberg, Germany.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 19.45 kDa 
• Atom Count: 1,171 
• Modeled Residue Count: 136 
• Deposited Residue Count: 163 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease ATP-binding subunit ClpC	A	163	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0  Gene Names: clpC, SAOUHSC_00505
UniProt
Find proteins for Q2G0P5 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2G0P5  Go to UniProtKB:  Q2G0P5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1JXU (Subject of Investigation/LOI)	B [auth A]	4-[6-[2-[(3~{R})-3,5-bis(4-methoxyphenyl)-3,4-dihydropyrazol-2-yl]-2-oxidanylidene-ethyl]sulfanyl-4-oxidanylidene-5~{H}-pyrazolo[3,4-d]pyrimidin-1-yl]benzenesulfonamide C30 H27 N7 O6 S2 HPWZZAFUKOJQNC-AREMUKBSSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.215 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.747	α = 90
b = 60.747	β = 90
c = 100.626	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-16 
Deposition Author(s): Kopp, J., Schwan, M., Sinning, I.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-09-16
  Type: Initial release
  
• Version 1.1: 2026-10-21
  Changes: Database references