SARS CoV-2 Mpro in complex with D-3-149
Liu, M., Huang, H.To be published.
8GVY
SARS CoV-2 Mpro in complex with D-3-149
- PDB DOI: https://doi.org/10.2210/pdb8GVY/pdb
- Classification: HYDROLASE
- Organism(s): Severe acute respiratory syndrome coronavirus 2, synthetic construct
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2022-09-16 Released: 2023-09-20
- Funding Organization(s): Not funded
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.271
- R-Value Work: 0.215
- R-Value Observed: 0.217
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
| Molecule | Chains | Sequence Length | Organism | Details | Image |
|---|---|---|---|---|---|
| 3C-like proteinase nsp5 | 306 | Severe acute respiratory syndrome coronavirus 2 | Mutation(s): 0 EC: 3.4.22.69 | ||
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 | ||||
| |||||
Find similar proteins by: Sequence | 3D Structure
| Molecule | Chains | Sequence Length | Organism | Details | Image |
|---|---|---|---|---|---|
| 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE | 4 | synthetic construct | Mutation(s): 0 | ||
| |||||
Small Molecules
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| 0A9 Query on 0A9 | B | L-PEPTIDE LINKING | C10 H13 N O2 | PHE | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.271
- R-Value Work: 0.215
- R-Value Observed: 0.217
- Space Group: I 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 45.015 | α = 90 |
| b = 53.095 | β = 100.85 |
| c = 113.098 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| SCALA | data scaling |
| PDB_EXTRACT | data extraction |
| CrysalisPro | data reduction |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
| Funding Organization | Location | Grant Number |
|---|---|---|
| Not funded | -- |
Revision History (Full details and data files)
- Version 1.0: 2023-09-20
Type: Initial release - Version 1.1: 2023-11-15
Changes: Data collection