Research workbench
SARS-cov-2 papain-like protease (plpro) bound to inhibitor XR8-65
Analyse SARS-cov-2 papain-like protease (plpro) bound to inhibitor XR8-65 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LOS
- Type
- protein
- Length
- 632 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-structural protein 3
- EC
- 3.4.19.12
- UniProt
- P0DTC1
- Ligands
- Y97, ZN, SO4, CL
- Pockets
- 8 · best druggability 0.49
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Non-structural protein 3 (EC 3.4.19.12) | protein | 316 | 26% helix, 35% strand | P0DTC1 |
Ligands and binding sites
- Y97 · 5-(azetidin-3-ylamino)-2-methyl-~{N}-[(1~{R})-1-[3-[5-[[[(3~{R})-oxolan-3-yl]amino]methyl]thiophen-2-yl]phenyl]ethyl]benzamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- CL · Chloride ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 168 | 0.49 | 0.77 | 29 | empty |
| 2 | 63 | 0.45 | 0.82 | 12 | empty |
| 3 | 173 | 0.45 | 0.75 | 26 | empty |
| 4 | 61 | 0.44 | 0.82 | 13 | empty |
| 5 | 80 | 0.39 | 0.78 | 19 | Y97 |
Interfaces
1 interface between chains.
- A–B · 301 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7LOS · SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-65 · 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 7LOS · PDBe 7LOS · UniProt P0DTC1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.