Download MendeleyChloroplast Protein GLYK Hijacked by Phytophthora Infestans Effector AVRvnt1 in Cytoplasm to Activate NLR
Hu, Q., Zhou, J., Yao, D., Xing, W.To be published.
7XPC | pdb_00007xpc
Complex structure of D-glycerate-3-kinase(GLYK) and AVRvnt1
- PDB DOI: https://doi.org/10.2210/pdb7XPC/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Solanum lycopersicum, Phytophthora infestans T30-4
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2022-05-04 Released: 2023-06-07
- Funding Organization(s): Not funded
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.31 Å
- R-Value Free: 0.317 (Depositor), 0.320 (DCC)
- R-Value Work: 0.293 (Depositor), 0.290 (DCC)
- R-Value Observed: 0.296 (Depositor)
wwPDB Validation 3D Report Full Report
This is version 1.1 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 |
| D-glycerate-3-kinase (GLYK) | 337 | Solanum lycopersicum | Mutation(s): 6 |  | |
UniProt | |||||
Find proteins for A0A3Q7FWS2 (Solanum lycopersicum) Explore A0A3Q7FWS2 Go to UniProtKB: A0A3Q7FWS2 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A3Q7FWS2 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| RxLR effector protein Avr-vnt11 | 84 | Phytophthora infestans T30-4 | Mutation(s): 0 Gene Names: Avr-vnt1, PITG_16294 |  | |
UniProt | |||||
Find proteins for D0NTY1 (Phytophthora infestans (strain T30-4)) Explore D0NTY1 Go to UniProtKB: D0NTY1 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | D0NTY1 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, C | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.31 Å
- R-Value Free: 0.317 (Depositor), 0.320 (DCC)
- R-Value Work: 0.293 (Depositor), 0.290 (DCC)
- R-Value Observed: 0.296 (Depositor)
Space Group: P 63
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 131.285 | α = 90 |
| b = 131.285 | β = 90 |
| c = 121.968 | γ = 120 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| PHENIX | phasing |
Entry History & Funding Information
Deposition Data
| Funding Organization | Location | Grant Number |
|---|---|---|
| Not funded | -- |
Revision History (Full details and data files)
- Version 1.0: 2023-06-07
Type: Initial release - Version 1.1: 2024-10-30
Changes: Data collection, Structure summary
