MolNFT v1 · #185759 · protein
Structure of SARS-cov-2 papain-like protease bound to N-(3-methoxy-4- hydroxy-ACETOPHENONE)THIOSEMICARBAZONE
7QCM · Papain-like protease NSP3: “Structure of SARS-cov-2 papain-like protease bound to N-(3-methoxy-4- hydroxy-ACETOPHENONE)THIOSEMICARBAZONE”. X-ray diffraction, 4 ligands (A3X, ZN, CL), 2 pockets (best druggability 0.38). MolNFT v1…
- PDB
- 7QCM
- 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
- A3X, ZN, CL, PO4
- Pockets
- 2 · best druggability 0.38
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
- A3X · N-(3-metoxy-4-hydroxy-acetophenone)thiosemicarbazone · ligand · chains A
- ZN · Zinc ion · metal · chains A
- CL · Chloride ion · ion · 3 copies · chains A
- PO4 · Phosphate ion · ion · 3 copies · chains A
- GOL · Glycerol · additive · 5 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 | 60 | 0.38 | 0.79 | 13 | A3X |
| 2 | 84 | 0.36 | 0.75 | 23 | empty |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 7QCM · Structure of SARS-CoV-2 Papain-like Protease bound to N-(3-methoxy-4-hydroxy-acetophe… · 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 7QCM · PDBe 7QCM · UniProt P0DTC1
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