Research workbench
Crystal structure of SARS-cov-2 main protease in complex with lon-wei- ADC59DF6-47
Analyse Crystal structure of SARS-cov-2 main protease in complex with lon-wei… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NW2
- Type
- protein
- Length
- 602 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0DTC1
- Ligands
- USZ, CL
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3C-like proteinase (EC 3.4.22.69) | protein | 301 | 24% helix, 30% strand | P0DTC1 |
Ligands and binding sites
- USZ · ~{N}-(4-~{tert}-butylphenyl)-~{N}-[(1~{R})-2-[2-(3-fluorophenyl)ethylamino]-2-oxidanylidene-1-pyridin-3-yl-ethyl]propanamide · ligand · chains A
- CL · Chloride ion · ion · chains A
- DMS · Dimethyl sulfoxide · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1003 | 0.77 | 0.79 | 83 | DMS |
| 2 | 632 | 0.68 | 0.77 | 101 | DMS |
| 3 | 251 | 0.55 | 0.77 | 31 | USZ |
| 4 | 161 | 0.48 | 0.77 | 27 | empty |
| 5 | 167 | 0.43 | 0.74 | 25 | DMS |
Interfaces
1 interface between chains.
- A–B · 1363 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7NW2 · Crystal Structure of SARS-CoV-2 main protease in complex with LON-WEI-adc59df6-47 · 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 P0DTC1
- Elsewhere: RCSB PDB 7NW2 · PDBe 7NW2 · UniProt P0DTC1
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