Download MendeleyTargeting Plasmodium falciparum GRP78: nucleoside analogues as agents against the malaria chaperone
Mrozek, A., Park, H.W.(2022) Frontiers In Molecular Bioscience
8D1W
Crystal structure of Plasmodium falciparum GRP78 in complex with (2R,3R,4S,5R)-2-(6-amino-8-((2-chlorobenzyl)amino)-9H-purin-9-yl)-5-(hydroxymethyl)tetrahydrofuran-3,4-diol
- PDB DOI: https://doi.org/10.2210/pdb8D1W/pdb
- Classification: CHAPERONE
- Organism(s): Plasmodium falciparum Palo Alto/Uganda
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2022-05-27 Released: 2023-05-31
- Funding Organization(s): Other private
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.221
- R-Value Work: 0.190
- R-Value Observed: 0.191
Starting Model: experimental
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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 |
| Chaperone DnaK | 397 | Plasmodium falciparum Palo Alto/Uganda | Mutation(s): 0 Gene Names: PFUGPA_02944 |  | |
UniProt | |||||
Find proteins for W4J0F1 (Plasmodium falciparum (isolate Palo Alto / Uganda)) Explore W4J0F1 Go to UniProtKB: W4J0F1 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | W4J0F1 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| HFY (Subject of Investigation/LOI) Query on HFY | B [auth A] | 8-{[(2-chlorophenyl)methyl]amino}adenosine C17 H19 Cl N6 O4 HXRSLQGBEUJHPP-XNIJJKJLSA-N |  | ||
| SO4 Query on SO4 | C [auth A], D [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.221
- R-Value Work: 0.190
- R-Value Observed: 0.191
- Space Group: P 65 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 84.288 | α = 90 |
| b = 84.288 | β = 90 |
| c = 292.218 | γ = 120 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| MOLREP | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2023-05-31 Deposition Author(s): Mrozek, A., Chen, Y., Antoshchenko, T., Park, H.W., Smil, D., Zepeda, C.A.V.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Other private | United States | -- |
Revision History (Full details and data files)
- Version 1.0: 2023-05-31
Type: Initial release - Version 1.1: 2023-10-25
Changes: Data collection, Refinement description
