Research workbench
Crystal structure of SARS coronavirus main protease in complex with an inhibitor shikonin
Analyse Crystal structure of SARS coronavirus main protease in complex with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EO8
- Type
- protein
- Length
- 596 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
- P0C6U8
- Ligands
- FNO
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3C-like proteinase (EC 3.4.22.69) | protein | 298 | 26% helix, 30% strand | P0C6U8 |
Ligands and binding sites
- FNO · 2-[(1R)-4-methyl-1-oxidanyl-pent-3-enyl]-5,8-bis(oxidanyl)naphthalene-1,4-dione · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 888 | 0.78 | 0.81 | 83 | empty |
| 2 | 113 | 0.41 | 0.76 | 30 | FNO |
| 3 | 149 | 0.39 | 0.73 | 33 | empty |
| 4 | 87 | 0.35 | 0.75 | 20 | empty |
| 5 | 53 | 0.33 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1016 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7EO8 · Crystal structure of SARS coronavirus main protease in complex with an inhibitor Shikonin · 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 P0C6U8
- Elsewhere: RCSB PDB 7EO8 · PDBe 7EO8 · UniProt P0C6U8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.