Research workbench
The crystal structure of SARS-cov-2 papain-like protease in complex with YM155
Analyse The crystal structure of SARS-cov-2 papain-like protease in complex with YM155 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D7L
- Type
- protein
- Length
- 624 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-structural protein 3
- EC
- 3.4.19.121, 3.4.22.-
- UniProt
- P0DTD1
- Ligands
- GXU, CFF, ZN, SO4
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Non-structural protein 3 (EC 3.4.19.121, 3.4.22.-) | protein | 312 | 27% helix, 36% strand | P0DTD1 |
Ligands and binding sites
- GXU · 1-(2-methoxyethyl)-2-methyl-3-(pyrazin-2-ylmethyl) benzo[f]benzimidazol-3-ium-4,9-dione · ligand · 5 copies · chains A, B
- CFF · Caffeine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 9 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.57 | 0.90 | 19 | empty |
| 2 | 57 | 0.53 | 0.88 | 17 | empty |
| 3 | 107 | 0.41 | 0.76 | 24 | empty |
| 4 | 92 | 0.40 | 0.77 | 20 | SO4, GOL |
| 5 | 60 | 0.34 | 0.77 | 16 | GXU |
Interfaces
1 interface between chains.
- A–B · 536 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7D7L · The crystal structure of SARS-CoV-2 papain-like protease in complex with YM155 · 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 P0DTD1
- Elsewhere: RCSB PDB 7D7L · PDBe 7D7L · UniProt P0DTD1
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