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The crystal structure of papain-like protease of SARS cov-2, C111S mutant, in complex with ebselen
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
- 7M1Y
- Type
- protein
- Length
- 626 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Papain-like protease
- EC
- 3.4.22.-
- UniProt
- P0DTC1
- Ligands
- 9JT, ZN, NA, IOD, CL
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Papain-like protease (EC 3.4.22.-) | protein | 314 | 26% helix, 37% strand | P0DTC1 |
| B | Papain-like protease (EC 3.4.22.-) | protein | 312 | 26% helix, 36% strand | P0DTC1 |
Ligands and binding sites
- 9JT · ~{N}-phenyl-2-selanyl-benzamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- IOD · Iodide ion · ion · 13 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- FMT · Formic acid · additive · 4 copies · chains A, B
- GOL · Glycerol · 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 | 317 | 0.54 | 0.75 | 39 | IOD |
| 2 | 100 | 0.44 | 0.79 | 24 | empty |
| 3 | 72 | 0.36 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 421 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7M1Y · 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
- Elsewhere: RCSB PDB 7M1Y · PDBe 7M1Y · UniProt P0DTC1
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