MolNFT v1 · #189000 · protein
The crystal structure of papain-like protease of SARS cov-2, C111S/D286N mutant, in complex with a LYS48-linked di-ubiquitin
7UV5 · Papain-like protease NSP3: “The crystal structure of papain-like protease of SARS cov-2, C111S/D286N mutant, in complex with a…”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.72). MolNFT v1 #189000 on GenesisL1…
- PDB
- 7UV5
- Type
- protein
- Length
- 429 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Papain-like protease NSP3; Ubiquitin
- EC
- 3.4.19.12, 3.4.22.-
- UniProt
- P0DTC1, P0CG48, P0CG47
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Papain-like protease NSP3 (EC 3.4.19.12, 3.4.22.-) | protein | 312 | 26% helix, 36% strand | P0DTC1 |
| B | Ubiquitin | protein | 76 | 20% helix, 34% strand | P0CG48 |
| C | Ubiquitin | protein | 41 | 20% helix, 27% strand | P0CG47 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 736 | 0.72 | 0.78 | 68 | empty |
| 2 | 358 | 0.66 | 0.80 | 47 | empty |
| 3 | 96 | 0.57 | 0.86 | 17 | empty |
| 4 | 95 | 0.42 | 0.78 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1065 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 491 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 36 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7UV5 · The crystal structure of Papain-Like Protease of SARS CoV-2, C111S/D286N mutant, in… · 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
- Every structure of UniProt P0CG48
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 7UV5 · PDBe 7UV5 · UniProt P0DTC1 · UniProt P0CG48 · UniProt P0CG47
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