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

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
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

N-terminal domain of ClpC from S. aureus

Kopp, J., Schwan, M., Sinning, I.

To be published.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2G0P5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1JXU( Subject of Investigation/LOI) Query on A1JXU Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2026-09-16
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.