Download MendeleyPanDDA analysis of COVID-19 main protease against the DSI-poised Fragment Library
Fearon, D., Powell, A.J., Douangamath, A., Owen, C.D., Wild, C., Krojer, T., Lukacik, P., Strain-Damerell, C.M., Walsh, M.A., von Delft, F.To be published.
5R84
PanDDA analysis group deposition -- Crystal Structure of COVID-19 main protease in complex with Z31792168
- DOI: 10.2210/pdb5R84/pdb
- Deposition Group: G_1002135 (changed state)
- Classification: HYDROLASE/HYDROLASE INHIBITOR
- Organism(s): Severe acute respiratory syndrome coronavirus 2
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2020-03-03 Released: 2020-03-11
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.83 Å
- R-Value Free: 0.293
- R-Value Work: 0.217
- R-Value Observed: 0.221
wwPDB Validation 3D Report Full Report
This is version 1.2 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 3C-like proteinase | A | 306 | Severe acute respiratory syndrome coronavirus 2 | Mutation(s): 0 Gene Names: rep, 1a-1b EC: 3.4.22 (PDB Primary Data), 3.4.22.69 (PDB Primary Data), 3.4.19.12 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt), 2.1.1 (UniProt) |  |
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1 | |||||
Protein Feature ViewExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GWS Query on GWS | A | 2-cyclohexyl-~{N}-pyridin-3-yl-ethanamide C13 H18 N2 O SIURWXONEBYXJD-UHFFFAOYSA-N |  | Ligand Interaction | |
| DMS Query on DMS | A | DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N |  | Ligand Interaction | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.83 Å
- R-Value Free: 0.293
- R-Value Work: 0.217
- R-Value Observed: 0.221
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 113.146 | α = 90 |
| b = 53.167 | β = 101.66 |
| c = 44.267 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| Aimless | data scaling |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| REFMAC | phasing |
Entry History
Deposition Data
- Deposited Date: 2020-03-03
- Released Date: 2020-03-11 Deposition Author(s): Fearon, D., Powell, A.J., Douangamath, A., Owen, C.D., Wild, C., Krojer, T., Lukacik, P., Strain-Damerell, C.M., Walsh, M.A., von Delft, F.
