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Crystal structure of SARS-cov-2 main protease A193S mutant in complex with nirmatrelvir
Analyse Crystal structure of SARS-cov-2 main protease A193S 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
- 8E1Y
- Type
- protein
- Length
- 604 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase NSP5
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- 4WI
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase NSP5 (EC 3.4.22.69) | protein | 302 | 25% helix, 29% strand | P0DTD1 |
| B | 3C-like proteinase NSP5 (EC 3.4.22.69) | protein | 302 | 24% 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 · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1066 | 0.77 | 0.79 | 89 | empty |
| 2 | 55 | 0.71 | 0.98 | 18 | DMS |
| 3 | 89 | 0.56 | 0.86 | 24 | DMS |
| 4 | 191 | 0.49 | 0.76 | 26 | 4WI |
| 5 | 197 | 0.47 | 0.75 | 34 | 4WI |
Interfaces
1 interface between chains.
- A–B · 1507 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 8E1Y · Crystal Structure of SARS-CoV-2 Main protease A193S mutant in complex with Nirmatrelvir · the same entry in another collection · chain A against A, TM-score 1.00
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 8E1Y · PDBe 8E1Y · UniProt P0DTD1
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