Research workbench
X-ray structure of SCOV2-plpro in complex with small molecule inhibitor
Analyse X-ray structure of SCOV2-plpro in complex with small molecule inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NT4
- Type
- protein
- Length
- 621 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, 3.4.22.-
- UniProt
- P0DTD1
- Ligands
- PRL, ZN, SO4
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-structural protein 3 (EC 3.4.19.12, 3.4.22.-) | protein | 308 | 25% helix, 32% strand | P0DTD1 |
| B | Non-structural protein 3 (EC 3.4.19.12, 3.4.22.-) | protein | 313 | 26% helix, 35% strand | P0DTD1 |
Ligands and binding sites
- PRL · Proflavin · ligand · 6 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 525 | 0.62 | 0.75 | 55 | PRL |
| 2 | 150 | 0.58 | 0.83 | 29 | empty |
| 3 | 121 | 0.45 | 0.77 | 20 | empty |
| 4 | 107 | 0.42 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 599 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7NT4 · X-ray structure of SCoV2-PLpro in complex with small molecule inhibitor · 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 7NT4 · PDBe 7NT4 · UniProt P0DTD1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.