MolNFT v1 · #187570 · protein
Btscov-RF1.2004 papain-like protease bound to the non-covalent inhibitor grl-0617
7SKQ · 3C-like proteinase: “Btscov-RF1.2004 papain-like protease bound to the non-covalent inhibitor grl-0617”. X-ray diffraction, 2 ligands (TTT, ZN), 2 pockets (best druggability 0.85). MolNFT v1 #187570 on GenesisL1: 3D structure…
- PDB
- 7SKQ
- Type
- protein
- Length
- 617 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.19.12, 3.4.22.69
- UniProt
- Q0QDZ2
- Ligands
- TTT, ZN
- Pockets
- 2 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.19.12, 3.4.22.69) | protein | 313 | 25% helix, 37% strand | Q0QDZ2 |
| B | 3C-like proteinase (EC 3.4.19.12, 3.4.22.69) | protein | 304 | 25% helix, 38% strand | Q0QDZ2 |
Ligands and binding sites
- TTT · 5-amino-2-methyl-N-[(1R)-1-naphthalen-1-ylethyl]benzamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1056 | 0.85 | 0.86 | 105 | TTT |
| 2 | 71 | 0.31 | 0.74 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1302 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 7SKQ · BtSCoV-Rf1.2004 Papain-Like protease bound to the non-covalent inhibitor GRL-0617 · 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 Q0QDZ2
- Elsewhere: RCSB PDB 7SKQ · PDBe 7SKQ · UniProt Q0QDZ2
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