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Structure of SARS-cov-2 papain-like protease bound to N-(2,5- dihydroxybenzylidene)-thiosemicarbazone
Analyse Structure of SARS-cov-2 papain-like protease bound to N-(2,5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QCK
- Type
- protein
- Length
- 315 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Papain-like protease NSP3
- EC
- 3.4.19.12, 3.4.22.-
- UniProt
- P0DTC1
- Ligands
- A7L, ZN, PO4, CL
- Pockets
- 3 · best druggability 0.40
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Papain-like protease NSP3 (EC 3.4.19.12, 3.4.22.-) | protein | 315 | 26% helix, 37% strand | P0DTC1 |
Ligands and binding sites
- A7L · N-(2,5-dihydroxybenzylidene)-thiosemicarbazone · ligand · chains A
- ZN · Zinc ion · metal · chains A
- PO4 · Phosphate ion · ion · 3 copies · chains A
- CL · Chloride ion · ion · 3 copies · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 89 | 0.40 | 0.78 | 24 | empty |
| 2 | 59 | 0.40 | 0.80 | 13 | A7L |
| 3 | 72 | 0.38 | 0.78 | 18 | empty |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 7QCK · Structure of SARS-CoV-2 Papain-like Protease bound to… · 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 7QCK · PDBe 7QCK · UniProt P0DTC1
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