Research workbench
X-ray structure of unbound porcine epidemic diarrhea virus 3CLPRO
Analyse X-ray structure of unbound porcine epidemic diarrhea virus 3CLPRO in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HYO
- Type
- protein
- Length
- 602 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pedv 3CLPRO
- UniProt
- A0A075EBR7
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pedv 3CLPRO | protein | 301 | 24% helix, 29% strand | A0A075EBR7 |
Ligands and binding sites
- IPA · Isopropyl alcohol · additive · 7 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 728 | 0.79 | 0.83 | 84 | empty |
| 2 | 529 | 0.66 | 0.78 | 60 | IPA |
| 3 | 454 | 0.66 | 0.78 | 53 | IPA, MPD |
| 4 | 249 | 0.55 | 0.77 | 31 | IPA, MPD |
| 5 | 248 | 0.52 | 0.76 | 30 | DMS |
Interfaces
1 interface between chains.
- A–B · 1677 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 5HYO · X-Ray Structure of Unbound Porcine Epidemic Diarrhea Virus 3CLpro · 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 A0A075EBR7
- Elsewhere: RCSB PDB 5HYO · PDBe 5HYO · UniProt A0A075EBR7
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