9P4H | pdb_00009p4h

Streptomyces thermoviolaceus ClpC2 C-terminal domain with bound Cyclomarin A

• PDB DOI: https://doi.org/10.2210/pdb9P4H/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Streptomyces thermoviolaceus, Streptomyces sp.
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-06-16 Released: 2026-06-10 
• Deposition Author(s): Anderson, H.R., Ogbonna, E.C., Kandel, P., Schmitz, K.R.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.174 (Depositor), 0.179 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.149 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Starting Model: experimental

Literature

Phosphoarginine modulates ClpC2 oligomerization and transcriptional regulation

Anderson, H.R., Ogbonna, E.C., Kandel, P., Schmitz, K.R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content 

• Total Structure Weight: 20.18 kDa 
• Atom Count: 1,440 
• Modeled Residue Count: 164 
• Deposited Residue Count: 189 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease ATP-binding subunit ClpC2	A	182	Streptomyces thermoviolaceus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LTU-WLU-ALA-WPA-VAL-MLE-WVL	B	7	Streptomyces sp.	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  5 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LTU	B	L-PEPTIDE LINKING	C16 H20 N2 O4		TRP
MLE	B	L-PEPTIDE LINKING	C7 H15 N O2		LEU
WLU	B	L-PEPTIDE LINKING	C7 H15 N O3		LEU
WPA	B	L-PEPTIDE LINKING	C10 H13 N O3		PHE
WVL	B	L-PEPTIDE LINKING	C8 H15 N O2		VAL

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002419	B	Cyclomarin A	Peptide-like / Antibiotic, Antimicrobial

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.174 (Depositor), 0.179 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.149 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.513	α = 90
b = 44.061	β = 109.36
c = 70.35	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-06-10 
Deposition Author(s): Anderson, H.R., Ogbonna, E.C., Kandel, P., Schmitz, K.R.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	S10OD26896
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P20GM104316
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI171196

Revision History  

• Version 1.0: 2026-06-10
  Type: Initial release