Download MendeleyDiscovery 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
9JXT | pdb_00009jxt
An aldehyde-containing intermediate of SufS in complex with (2R,3R)-3-ethoxycarbonylaziridine-2-carboxylic acid
- PDB DOI: https://doi.org/10.2210/pdb9JXT/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
- Funding Organization(s): Japan Society for the Promotion of Science (JSPS), New Energy and Industrial Technology Development Organization (NEDO)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.212 (Depositor), 0.212 (DCC)
- R-Value Work: 0.174 (Depositor), 0.174 (DCC)
- R-Value Observed: 0.176 (Depositor)
Starting Model: experimental
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wwPDB Validation 3D Report Full Report
This is version 1.0 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cysteine desulfurase SufS | 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 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O32164 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| A1L40 (Subject of Investigation/LOI) Query on A1L40 | C [auth A] | (2~{S})-2-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-3-oxidanylidene-propanoic acid C11 H13 N2 O8 P GAMDABAFAVQUPR-BIMOUXMDSA-N |  | ||
| PEG Query on PEG | B [auth A] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.212 (Depositor), 0.212 (DCC)
- R-Value Work: 0.174 (Depositor), 0.174 (DCC)
- R-Value Observed: 0.176 (Depositor)
Space Group: P 31 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 92.7 | α = 90 |
| b = 92.7 | β = 90 |
| c = 128.32 | γ = 120 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| XSCALE | data scaling |
| XDS | data reduction |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2025-07-16 Deposition Author(s): Nakamura, R., Fujishiro, T.
| 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 (Full details and data files)
- Version 1.0: 2025-07-16
Type: Initial release
