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Crystal Structure of SARS-CoV-2 Main protease A193T mutant in complex with Nirmatrelvir
Analyse Crystal Structure of SARS-CoV-2 Main protease A193T mutant in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8DZA
- Type
- protein
- Length
- 606 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.961
- Source
- Severe acute respiratory syndrome coronavirus 2
- Molecule
- 3C-like proteinase nsp5
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- 4WI
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · resolution 1.961 · 2 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase nsp5 (EC 3.4.22.69) | protein | 301 | 26% helix, 29% strand | P0DTD1 |
| B | 3C-like proteinase nsp5 (EC 3.4.22.69) | protein | 305 | 27% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- 4WI · (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide · ligand · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 5 copies · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1050 | 0.77 | 0.79 | 90 | DMS |
| 2 | 254 | 0.58 | 0.78 | 41 | DMS |
| 3 | 217 | 0.51 | 0.76 | 30 | 4WI |
| 4 | 188 | 0.49 | 0.76 | 29 | 4WI |
| 5 | 123 | 0.38 | 0.73 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1495 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand, additive adduct).
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 8DZA · PDBe 8DZA · UniProt P0DTD1
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