Download MendeleyStructural basis for the recognition of type-2 N-degron by PRT1 plant N-recognin
Yang, W.S., Song, H.K.To be published.
8ZG8 | pdb_00008zg8
ZZ-domain of the Arabidopsis thaliana E3 ubiquitin-protein ligase PRT1
- PDB DOI: https://doi.org/10.2210/pdb8ZG8/pdb
- Classification: LIGASE
- Organism(s): Arabidopsis thaliana
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2024-05-09 Released: 2025-05-14
- Funding Organization(s): National Research Foundation (NRF, Korea)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.74 ?
- R-Value Free: 0.279 (Depositor), 0.283 (DCC)
- R-Value Work: 0.235 (Depositor), 0.240 (DCC)
- R-Value Observed: 0.239 (Depositor)
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 |
| E3 ubiquitin-protein ligase PRT1 | 64 | Arabidopsis thaliana | Mutation(s): 0 Gene Names: PRT1, At3g24800, K7P8.9 EC: 2.3.2.27 |  | |
UniProt | |||||
Find proteins for Q8LBL5 (Arabidopsis thaliana) Explore Q8LBL5 Go to UniProtKB: Q8LBL5 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q8LBL5 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ZN (Subject of Investigation/LOI) Query on ZN | B [auth A], C [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.74 ?
- R-Value Free: 0.279 (Depositor), 0.283 (DCC)
- R-Value Work: 0.235 (Depositor), 0.240 (DCC)
- R-Value Observed: 0.239 (Depositor)
Space Group: P 62 2 2
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 78.03 | ¦Á = 90 |
| b = 78.03 | ¦Â = 90 |
| c = 70.452 | ¦Ă = 120 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| XDS | data scaling |
| PHENIX | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2025-05-14 Deposition Author(s): Yang, W.S., Song, H.K.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Research Foundation (NRF, Korea) | Korea, Republic Of | 2020R1A2C3008285 |
| National Research Foundation (NRF, Korea) | Korea, Republic Of | 2021M3A9I4030068 |
| National Research Foundation (NRF, Korea) | Korea, Republic Of | 2022M3A9G8082638 |
Revision History (Full details and data files)
- Version 1.0: 2025-05-14
Type: Initial release
