Research workbench
SARS cov-2 plpro in complex with inhibitor 3K
Analyse SARS cov-2 plpro in complex with inhibitor 3K in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TZJ
- Type
- protein
- Length
- 601 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Papain-like protease
- EC
- 3.4.19.12
- UniProt
- P0DTC1
- Ligands
- S88, ZN
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Papain-like protease (EC 3.4.19.12) | protein | 300 | 28% helix, 32% strand | P0DTC1 |
| B | Papain-like protease (EC 3.4.19.12) | protein | 301 | 28% helix, 33% strand | P0DTC1 |
Ligands and binding sites
- S88 · N-[(3-fluorophenyl)methyl]-1-[(1R)-1-naphthalen-1-ylethyl]piperidine-4-carboxamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 9 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 2 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 562 | 0.66 | 0.76 | 73 | empty |
| 2 | 123 | 0.46 | 0.78 | 23 | S88, DMS |
| 3 | 119 | 0.44 | 0.77 | 24 | S88 |
| 4 | 107 | 0.40 | 0.76 | 15 | ZN |
| 5 | 78 | 0.38 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 329 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7TZJ · SARS CoV-2 PLpro in complex with inhibitor 3k · 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 7TZJ · PDBe 7TZJ · UniProt P0DTC1
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