Download MendeleyDeciphering Antiviral Mechanisms of Herbacetin and Caffeic acid phenethyl ester against Chikungunya and Dengue virus, with insights into Dengue methyltransferase-CAPE crystal structure
Bhutkar, M., Kumar, A., Tomar, S., Kumar, P.To be published.
8KDZ | pdb_00008kdz
DENGUE 3 NS5 METHYLTRANSFERASE BOUND TO S-Adenosyl-L-homocysteine and Caffeic acid phenethyl ester
- PDB DOI: https://doi.org/10.2210/pdb8KDZ/pdb
- Classification: VIRAL PROTEIN
- Organism(s): dengue virus type 3
- Expression System: Escherichia coli BL21
- Mutation(s): No
- Deposited: 2023-08-10 Released: 2025-02-19
- Funding Organization(s): Indian Council of Medical Research
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.273 (Depositor), 0.274 (DCC)
- R-Value Work: 0.231 (Depositor), 0.232 (DCC)
Starting Model: experimental
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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 |
| methyltransferase | 284 | dengue virus type 3 | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for A9LID6 (dengue virus type 3) Explore A9LID6 Go to UniProtKB: A9LID6 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A9LID6 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SAH Query on SAH | C [auth A], F [auth B] | S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N |  | ||
| QAP (Subject of Investigation/LOI) Query on QAP | D [auth A], E [auth A] | 2-phenylethyl (2E)-3-(3,4-dihydroxyphenyl)prop-2-enoate C17 H16 O4 SWUARLUWKZWEBQ-VQHVLOKHSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.273 (Depositor), 0.274 (DCC)
- R-Value Work: 0.231 (Depositor), 0.232 (DCC)
Space Group: P 2 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 51.648 | α = 90 |
| b = 60.722 | β = 90 |
| c = 184.36 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| CrysalisPro | data reduction |
| CrysalisPro | data scaling |
| MOLREP | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2025-02-19 Deposition Author(s): Bhutkar, M., Kumar, A., Tomar, S., Kumar, P.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Indian Council of Medical Research | India | -- |
Revision History (Full details and data files)
- Version 1.0: 2025-02-19
Type: Initial release
