Research workbench
Papain-like protease of SARS cov-2, C111S mutant, in complex with JUN9-84-3 inhibitor
Analyse Papain-like protease of SARS cov-2, C111S mutant, in complex with JUN9-84-3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SQE
- Type
- protein
- Length
- 941 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Papain-like protease
- EC
- 3.4.19.12
- UniProt
- P0DTC1
- Ligands
- JWX, ZN, CL
- Pockets
- 11 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Papain-like protease (EC 3.4.19.12) | protein | 314 | 26% helix, 36% strand | P0DTC1 |
| B | Papain-like protease (EC 3.4.19.12) | protein | 316 | 26% helix, 36% strand | P0DTC1 |
| C | Papain-like protease (EC 3.4.19.12) | protein | 311 | 27% helix, 35% strand | P0DTC1 |
Ligands and binding sites
- JWX · (1R)-N-[(1H-indol-3-yl)methyl]-N-methyl-1-(naphthalen-1-yl)ethan-1-amine · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 6 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1168 | 0.88 | 0.89 | 124 | JWX |
| 2 | 425 | 0.77 | 0.86 | 58 | EDO, CL |
| 3 | 491 | 0.71 | 0.81 | 52 | CL |
| 4 | 281 | 0.62 | 0.80 | 50 | empty |
| 5 | 132 | 0.46 | 0.77 | 24 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1608 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 381 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 303 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7SQE · Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with Jun9-84-3 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 P0DTC1
- Elsewhere: RCSB PDB 7SQE · PDBe 7SQE · UniProt P0DTC1
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