MolNFT v1 · #181144 · protein
SARS-cov-2 papain-like protease (plpro) bound to inhibitor XR8-69
7LLZ · Non-structural protein 3: “SARS-cov-2 papain-like protease (plpro) bound to inhibitor XR8-69”. X-ray diffraction, 3 ligands (Y61, ZN, SO4), 7 pockets (best druggability 0.50). MolNFT v1 #181144 on GenesisL1: 3D structure, binding…
- PDB
- 7LLZ
- Type
- protein
- Length
- 632 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-structural protein 3
- EC
- 3.4.19.12
- UniProt
- P0DTC1
- Ligands
- Y61, ZN, SO4
- Pockets
- 7 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Non-structural protein 3 (EC 3.4.19.12) | protein | 316 | 26% helix, 35% strand | P0DTC1 |
Ligands and binding sites
- Y61 · N-[(1R)-1-(3-{5-[(acetylamino)methyl]thiophen-2-yl}phenyl)ethyl]-5-[(azetidin-3-yl)amino]-2-methylbenzamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.50 | 0.80 | 23 | empty |
| 2 | 145 | 0.44 | 0.75 | 26 | empty |
| 3 | 58 | 0.42 | 0.82 | 12 | empty |
| 4 | 81 | 0.39 | 0.78 | 21 | Y61 |
| 5 | 120 | 0.39 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 307 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7LLZ · SARS-CoV-2 papain-like protease (PLpro) bound to inhibitor XR8-69 · 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 7LLZ · PDBe 7LLZ · UniProt P0DTC1
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