SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor dFFCit-yne
Lockbaum, G.J., Schiffer, C.A.To be published.
7MAV
SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor dFFCit-yne
- PDB DOI: https://doi.org/10.2210/pdb7MAV/pdb
- Classification: HYDROLASE/HYDROLASE INHIBITOR
- Organism(s): Severe acute respiratory syndrome coronavirus 2
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2021-03-31 Released: 2022-10-12
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.91 Å
- R-Value Free: 0.244
- R-Value Work: 0.201
- R-Value Observed: 0.203
Starting Model: experimental
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This is version 1.2 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
| Molecule | Chains | Sequence Length | Organism | Details | Image |
|---|---|---|---|---|---|
| 3C-like proteinase | 306 | Severe acute respiratory syndrome coronavirus 2 | Mutation(s): 0 Gene Names: rep, 1a-1b 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 | ||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| YVY (Subject of Investigation/LOI) Query on YVY | C [auth A], D [auth B] | N-{3-[(prop-2-yn-1-yl)oxy]propanoyl}-D-phenylalanyl-N-[(3S)-6-(carbamoylamino)-2-oxohexan-3-yl]-L-phenylalaninamide C31 H39 N5 O6 VYPOUUBVMAOAGP-VJGNERBWSA-N | |||
Biologically Interesting Molecules (External Reference) 1 Unique
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
|---|---|---|---|---|---|
| PRD_002472 (YVY) Query on PRD_002472 | C [auth A], D [auth B] | N-{3-[(prop-2-yn-1-yl)oxy]propanoyl}-D-phenylalanyl-N-[(3S)-6-(carbamoylamino)-2-oxohexan-3-yl]-L-phenylalaninamide | Peptide-like / Inhibitor | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.91 Å
- R-Value Free: 0.244
- R-Value Work: 0.201
- R-Value Observed: 0.203
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 49.98 | α = 90 |
| b = 106.46 | β = 104.6 |
| c = 53.57 | γ = 90 |
| Software Name | Purpose |
|---|---|
| XSCALE | data scaling |
| PHASER | phasing |
| PHENIX | refinement |
| Coot | model building |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
Entry History & Funding Information
Deposition Data
- Released Date: 2022-10-12 Deposition Author(s): Lockbaum, G.J., Schiffer, C.A.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | P01-GM109767 |
Revision History (Full details and data files)
- Version 1.0: 2022-10-12
Type: Initial release - Version 1.1: 2023-10-18
Changes: Data collection, Refinement description - Version 1.2: 2024-10-16
Changes: Structure summary