Research workbench
SARS cov-2 plpro in complex with ISG15 C-terminal domain propargylamide
Analyse SARS cov-2 plpro in complex with ISG15 C-terminal domain propargylamide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XA9
- Type
- protein
- Length
- 1,168 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-structural protein 3; ISG15 ctd-propargylamide
- EC
- 3.4.19.121, 3.4.22.-
- UniProt
- P0DTD1, P05161
- Ligands
- AYE, ZN
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Non-structural protein 3 (EC 3.4.19.121, 3.4.22.-) | protein | 313 | 26% helix, 37% strand | P0DTD1 |
| B | ISG15 ctd-propargylamide | protein | 79 | 20% helix, 34% strand | P05161 |
| D, F | ISG15 ctd-propargylamide | protein | 78 | 24% helix, 35% strand | P05161 |
| E | Non-structural protein 3 (EC 3.4.19.121, 3.4.22.-) | protein | 307 | 26% helix, 37% strand | P0DTD1 |
Ligands and binding sites
- AYE · prop-2-en-1-amine · ligand · 3 copies · chains A, B, C, D, E, F
- ZN · Zinc ion · metal · 3 copies · chains A, C, E
- GOL · Glycerol · additive · 8 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1146 | 0.77 | 0.79 | 108 | AYE |
| 2 | 511 | 0.70 | 0.80 | 59 | empty |
| 3 | 482 | 0.69 | 0.80 | 47 | empty |
| 4 | 379 | 0.63 | 0.78 | 43 | empty |
| 5 | 193 | 0.47 | 0.75 | 33 | empty |
Interfaces
9 interfaces between chains.
- A–B · 889 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 884 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 873 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 623 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 377 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 6XA9 · SARS CoV-2 PLpro in complex with ISG15 C-terminal domain propargylamide · the same entry in another collection · chain F against F, TM-score 1.00
- P05161 · AlphaFold monomer V2.0 prediction for ubiquitin-like protein ISG15 (P05161) · a predicted model of the same protein · chain B against A, TM-score 0.96
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
- Every structure of UniProt P05161
- Elsewhere: RCSB PDB 6XA9 · PDBe 6XA9 · UniProt P0DTD1 · UniProt P05161
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