MolNFT v1 · #185755 · protein
Structure of SARS-cov-2 papain-like protease bound to N-(3,5- dimethoxy-4-HYDROXYBENZYLIDEN)THIOSEMICARBAZONE
7QCH · Papain-like protease NSP3: “Structure of SARS-cov-2 papain-like protease bound to N-(3,5- dimethoxy-4-HYDROXYBENZYLIDEN)THIOSEMICARBAZONE”. X-ray diffraction, 4 ligands (A5I, ZN, PO4), 2 pockets (best druggability 0.45). MolNFT v1…
- PDB
- 7QCH
- 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
- A5I, ZN, PO4, CL
- Pockets
- 2 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Papain-like protease NSP3 (EC 3.4.19.12, 3.4.22.-) | protein | 315 | 27% helix, 36% strand | P0DTC1 |
Ligands and binding sites
- A5I · N-(3,5-dimetoxy-4-hydroxybenzyliden)thiosemicarbazone · ligand · chains A
- ZN · Zinc ion · metal · chains A
- PO4 · Phosphate ion · ion · 5 copies · chains A
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.45 | 0.83 | 13 | A5I |
| 2 | 71 | 0.38 | 0.78 | 19 | empty |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 7QCH · 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 7QCH · PDBe 7QCH · UniProt P0DTC1
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