MolNFT v1 · #168222 · protein
The crystal structure of papain-like protease of SARS cov-2
6W9C · Non-structural protein 3: “The crystal structure of papain-like protease of SARS cov-2”. X-ray diffraction, 2 ligands (ZN, CL), 9 pockets (best druggability 0.76). MolNFT v1 #168222 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6W9C
- Type
- protein
- Length
- 926 residues
- Chains
- 3
- 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
- ZN, CL
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-structural protein 3 (EC 3.4.19.12) | protein | 310 | 26% helix, 35% strand | P0DTC1 |
| B | Non-structural protein 3 (EC 3.4.19.12) | protein | 307 | 26% helix, 35% strand | P0DTC1 |
| C | Non-structural protein 3 (EC 3.4.19.12) | protein | 309 | 26% helix, 35% strand | P0DTC1 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.76 | 0.78 | 90 | empty |
| 2 | 448 | 0.63 | 0.76 | 37 | empty |
| 3 | 104 | 0.48 | 0.80 | 17 | empty |
| 4 | 85 | 0.47 | 0.81 | 15 | empty |
| 5 | 89 | 0.45 | 0.80 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–C · 423 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 408 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 360 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6W9C · The crystal structure of papain-like protease of SARS CoV-2 · 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 6W9C · PDBe 6W9C · UniProt P0DTC1
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