Crystal structure of SARS-Cov-2 main protease G15S mutant in complex with inhibitor YH-53
Zeng, P., Zhang, J., Li, J.To be published.
8HQF
Crystal structure of SARS-Cov-2 main protease G15S mutant in complex with inhibitor YH-53
- PDB DOI: https://doi.org/10.2210/pdb8HQF/pdb
- Classification: VIRAL PROTEIN/INHIBITOR
- Organism(s): Severe acute respiratory syndrome coronavirus 2
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2022-12-13 Released: 2024-01-31
- Funding Organization(s): Not funded
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.51 Å
- R-Value Free: 0.230
- R-Value Work: 0.208
- R-Value Observed: 0.209
Starting Model: experimental
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This is version 1.0 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
| Molecule | Chains | Sequence Length | Organism | Details | Image |
|---|---|---|---|---|---|
| Non-structural protein 7 | 299 | Severe acute respiratory syndrome coronavirus 2 | Mutation(s): 1 Gene Names: rep, 1a-1b | ||
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1 | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P0DTD1 | ||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| HUR (Subject of Investigation/LOI) Query on HUR | C [auth A], D [auth B] | N-[(2S)-1-[[(2S)-1-(1,3-benzothiazol-2-yl)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-methoxy-1H-indole-2-carboxamide C30 H33 N5 O5 S JBLLRCOZJMVOAE-HSQYWUDLSA-N | |||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.51 Å
- R-Value Free: 0.230
- R-Value Work: 0.208
- R-Value Observed: 0.209
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 55.381 | α = 90 |
| b = 99.44 | β = 108.253 |
| c = 59.461 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| XDS | data scaling |
| 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: 2024-01-31
Type: Initial release