Research workbench
Porcine epidemic diarrhea virus papain-like protease 2 C44S mutant in complex with mono ubiquitin
Analyse Porcine epidemic diarrhea virus papain-like protease 2 C44S mutant in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7F0U
- Type
- protein
- Length
- 586 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Papain-like protease 2; Ubiquitin
- UniProt
- A0A0U2C377, P62992
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Papain-like protease 2 | protein | 217 | 27% helix, 36% strand | A0A0U2C377 |
| C, D | Ubiquitin | protein | 76 | 24% helix, 33% strand | P62992 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
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 | 106 | 0.61 | 0.87 | 21 | empty |
| 2 | 313 | 0.58 | 0.77 | 52 | empty |
| 3 | 164 | 0.49 | 0.78 | 31 | empty |
| 4 | 64 | 0.36 | 0.78 | 17 | empty |
| 5 | 52 | 0.24 | 0.72 | 13 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1067 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 582 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 421 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 11 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7F0U · porcine epidemic diarrhea virus papain-like protease 2 C44S mutant in complex with mono… · the same entry in another collection · chain A against A, TM-score 1.00
- P62992 · AlphaFold monomer V2.0 prediction for ubiquitin-40S ribosomal protein S27A (P62992) · a predicted model of the same protein · chain C against A, TM-score 0.95
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 A0A0U2C377
- Every structure of UniProt P62992
- Elsewhere: RCSB PDB 7F0U · PDBe 7F0U · UniProt A0A0U2C377 · UniProt P62992
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