Research workbench
3C-like protease from Southampton virus complexed with XST00000642b.
Analyse 3C-like protease from Southampton virus complexed with XST00000642b. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TCF
- Type
- protein
- Length
- 343 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.79
- Source
- Southampton virus (serotype 3)
- Molecule
- Genome polyprotein
- EC
- 3.6.1.15, 3.4.22.66, 2.7.7.48
- UniProt
- Q04544
- Ligands
- N1E, PO4
- Pockets
- 3 · best druggability 0.37
Structure
x-ray diffraction · resolution 1.79 · 2 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Genome polyprotein (EC 3.6.1.15, 3.4.22.66, 2.7.7.48) | protein | 172 | 9% helix, 51% strand | Q04544 |
| B | Genome polyprotein (EC 3.6.1.15, 3.4.22.66, 2.7.7.48) | protein | 171 | 8% helix, 50% strand | Q04544 |
Ligands and binding sites
- N1E · methyl quinoline-6-carboxylate · ligand · chains B
- PO4 · Phosphate ion · ion · chains A
- DMS · Dimethyl sulfoxide · additive · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.37 | 0.77 | 24 | empty |
| 2 | 70 | 0.37 | 0.78 | 20 | empty |
| 3 | 53 | 0.35 | 0.79 | 10 | DMS |
Interfaces
1 interface between chains.
- A–B · 957 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6TCF · 3C-like protease from southampton virus complexed with XST00000642B. · 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 Q04544
- Elsewhere: RCSB PDB 6TCF · PDBe 6TCF · UniProt Q04544
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