Research workbench
Crystal structure of SARS-cov-2 main protease G143S mutant in complex with nirmatrelvir
Analyse Crystal structure of SARS-cov-2 main protease G143S 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
- 8DZ9
- Type
- protein
- Length
- 1,210 residues
- Chains
- 4
- 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
- 15 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | 3C-like proteinase NSP5 (EC 3.4.22.69) | protein | 302 | 26% helix, 29% strand | P0DTD1 |
| D | 3C-like proteinase NSP5 (EC 3.4.22.69) | protein | 304 | 25% 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 · 4 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1074 | 0.77 | 0.79 | 88 | empty |
| 2 | 1031 | 0.76 | 0.79 | 79 | empty |
| 3 | 782 | 0.75 | 0.79 | 79 | empty |
| 4 | 224 | 0.54 | 0.77 | 30 | 4WI |
| 5 | 199 | 0.51 | 0.77 | 29 | 4WI |
Interfaces
3 interfaces between chains.
- C–D · 1459 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 1420 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 636 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 8DZ9 · Crystal Structure of SARS-CoV-2 Main protease G143S 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 8DZ9 · PDBe 8DZ9 · UniProt P0DTD1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.