Research workbench
SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor dFFR-yne
Analyse SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor dFFR-yne in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MAU
- Type
- protein
- Length
- 605 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.95
- Source
- Severe acute respiratory syndrome coronavirus 2
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- YVP, SO4
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · resolution 1.95 · 2 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 305 | 26% helix, 29% strand | P0DTD1 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 300 | 25% helix, 30% strand | P0DTD1 |
Ligands and binding sites
- YVP · N-{3-[(prop-2-yn-1-yl)oxy]propanoyl}-D-phenylalanyl-N-[(3S)-6-carbamimidamido-2-oxohexan-3-yl]-L-phenylalaninamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- DIO · 1,4-diethylene dioxide · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 969 | 0.76 | 0.79 | 84 | SO4 |
| 2 | 213 | 0.47 | 0.75 | 30 | DIO, YVP |
| 3 | 197 | 0.46 | 0.74 | 24 | YVP |
| 4 | 97 | 0.37 | 0.75 | 22 | empty |
| 5 | 100 | 0.37 | 0.75 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1486 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0DTD1
- Elsewhere: RCSB PDB 7MAU · PDBe 7MAU · UniProt P0DTD1
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