9JX7 | pdb_00009jx7

SufS in complex with (2R,3R)-3-ethoxycarbonylaziridine-2-carboxylic acid

• PDB DOI: https://doi.org/10.2210/pdb9JX7/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-10-11 Released: 2025-07-16 
• Deposition Author(s): Fujishiro, T., Nakamura, R.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), New Energy and Industrial Technology Development Organization (NEDO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.186 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

Discovery of an Aziridine-Based Inhibitor That Targets Cysteine Desulfurase Type II SufS via High-Throughput X-ray Crystallography

Fujishiro, T., Otsuka, H., Nakamura, R., Fujihara, T.

(2025) ACS Med Chem Lett 

• DOI: https://doi.org/10.1021/acsmedchemlett.5c00168

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

Macromolecule Content 

• Total Structure Weight: 47.36 kDa 
• Atom Count: 3,532 
• Modeled Residue Count: 406 
• Deposited Residue Count: 419 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine desulfurase SufS	A	419	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: sufS, csd, yurW, BSU32690 EC: 2.8.1.7
UniProt
Find proteins for O32164 (Bacillus subtilis (strain 168)) Explore O32164  Go to UniProtKB:  O32164

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1L4Z (Subject of Investigation/LOI)	F [auth A]	2-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]propanedioic acid C11 H13 N2 O9 P NZWIGLKAYRQNJI-QLKAYGNNSA-N
PEG	B [auth A], C [auth A], D [auth A], E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.186 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.97	α = 90
b = 92.97	β = 90
c = 129.9	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-16 
Deposition Author(s): Fujishiro, T., Nakamura, R.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	23H04542
New Energy and Industrial Technology Development Organization (NEDO)	Japan	22100875-0

Revision History  

• Version 1.0: 2025-07-16
  Type: Initial release