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The crystal structure of papain-like protease of SARS cov-2, C111S mutant, in complex with a LYS48-linked di-ubiquitin
Analyse The crystal structure of papain-like protease of SARS cov-2, C111S mutant, in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RBR
- Type
- protein
- Length
- 389 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Papain-like protease; Ubiquitin
- EC
- 3.4.19.12
- UniProt
- P0DTC1, P0CG47
- Ligands
- ZN, CL
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Papain-like protease (EC 3.4.19.12) | protein | 313 | 26% helix, 36% strand | P0DTC1 |
| B | Ubiquitin | protein | 76 | 24% helix, 34% strand | P0CG47 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 495 | 0.72 | 0.81 | 61 | empty |
| 2 | 63 | 0.48 | 0.84 | 14 | empty |
| 3 | 97 | 0.42 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1071 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 7RBR · The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex… · 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 P0CG47
- Elsewhere: RCSB PDB 7RBR · PDBe 7RBR · UniProt P0DTC1 · UniProt P0CG47
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