Download MendeleyNovel type II toxin-antitoxin systems with VapD-like proteins
Gilep, K., Popov, A., Bikmetov, D., Tagami, S., Dubiley, S., Severinov, K.To be published.
9KAN
Crystal structure of the C. jejuni VapD-VapW toxin-antitoxin complex
- PDB DOI: https://doi.org/10.2210/pdb9KAN/pdb
- Classification: TOXIN/ANTITOXIN
- Organism(s): Campylobacter jejuni
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2024-10-29 Released: 2025-02-12
- Funding Organization(s): Not funded
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 ?
- R-Value Free: 0.249 (Depositor), 0.249 (DCC)
- R-Value Work: 0.221 (Depositor), 0.221 (DCC)
- R-Value Observed: 0.222 (Depositor)
Starting Model: in silico
View more details
wwPDB Validation 3D Report Full Report
This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Vapd | 138 | Campylobacter jejuni | Mutation(s): 0 Gene Names: BCB58_08990, BFD99_07080, C1418_08930, E7N58_08980, E8P16_09265, F0J89_08805, GNO00_08035, GSU20_08840 |  | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| VapW antitoxin | 135 | Campylobacter jejuni | Mutation(s): 0 Gene Names: B7A03_08765, BCB58_08995, BFD99_07085, C1418_08935, E7N58_08985, E8P16_09270, F0J89_08810, FBF07_08610, GNO00_08040, GSU20_08845 |  | |
UniProt | |||||
Find proteins for A0A3Z8NCW8 (Campylobacter jejuni) Explore A0A3Z8NCW8 Go to UniProtKB: A0A3Z8NCW8 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A3Z8NCW8 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SO4 Query on SO4 | E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 ?
- R-Value Free: 0.249 (Depositor), 0.249 (DCC)
- R-Value Work: 0.221 (Depositor), 0.221 (DCC)
- R-Value Observed: 0.222 (Depositor)
Space Group: C 2 2 21
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 89.578 | ¦Á = 90 |
| b = 94.807 | ¦Â = 90 |
| c = 137.684 | ¦Ă = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| PHASER | phasing |
| XDS | data scaling |
Entry History & Funding Information
Deposition Data
- Released Date: 2025-02-12 Deposition Author(s): Popov, A., Gilep, K., Tagami, S.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Not funded | -- |
Revision History (Full details and data files)
- Version 1.0: 2025-02-12
Type: Initial release
