Research workbench
3C-like protease from southampton virus complexed with FMOPL000363A.
Analyse 3C-like protease from southampton virus complexed with FMOPL000363A. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TBO
- Type
- protein
- Length
- 344 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein
- EC
- 3.6.1.15, 3.4.22.66, 2.7.7.48
- UniProt
- Q04544
- Ligands
- N0E, PO4
- Pockets
- 3 · best druggability 0.37
Structure
x-ray diffraction · 2 distinct chains · 7% 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 | 8% helix, 51% strand | Q04544 |
| B | Genome polyprotein (EC 3.6.1.15, 3.4.22.66, 2.7.7.48) | protein | 172 | 7% helix, 50% strand | Q04544 |
Ligands and binding sites
- N0E · ~{N}-(4-hydroxyphenyl)-3-phenyl-propanamide · ligand · chains A, B
- PO4 · Phosphate ion · ion · chains B
- DMS · Dimethyl sulfoxide · additive · 3 copies · 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 | 59 | 0.37 | 0.79 | 13 | DMS |
| 2 | 86 | 0.36 | 0.76 | 21 | empty |
| 3 | 54 | 0.26 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 972 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6TBO · 3C-like protease from Southampton virus complexed with FMOPL000363a. · 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 6TBO · PDBe 6TBO · UniProt Q04544
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