Research workbench
3C-like protease from southampton virus complexed with FMOPL000582A.
Analyse 3C-like protease from southampton virus complexed with FMOPL000582A. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6T49
- Type
- protein
- Length
- 342 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
- MH5, PO4
- Pockets
- 2 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 51% 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 | 170 | 9% helix, 51% strand | Q04544 |
Ligands and binding sites
- MH5 · 3-[(5-methylthiophen-2-yl)methylamino]benzoic acid · ligand · chains A
- PO4 · Phosphate ion · ion · chains B
- DMS · Dimethyl sulfoxide · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 75 | 0.42 | 0.80 | 24 | MH5, DMS |
| 2 | 95 | 0.39 | 0.77 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 851 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6T49 · 3C-like protease from Southampton virus complexed with FMOPL000582a. · 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 6T49 · PDBe 6T49 · UniProt Q04544
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