MolNFT v1 · #125431 · protein
Structure of deformed wing virus, a honeybee pathogen
5L8Q · VP1: “Structure of deformed wing virus, a honeybee pathogen”. Electron microscopy, 1 ligand (U), 9 pockets (best druggability 0.61). MolNFT v1 #125431 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5L8Q
- Type
- protein
- Length
- 899 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; VP2; VP3
- UniProt
- L0CTV4, E0YTW0, Q7TG18
- Ligands
- U
- Pockets
- 9 · best druggability 0.61
Structure
electron microscopy · 3 distinct chains · 11% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 252 | 10% helix, 19% strand | L0CTV4 |
| B | VP2 | protein | 250 | 14% helix, 24% strand | E0YTW0 |
| C | VP3 | protein | 397 | 9% helix, 27% strand | Q7TG18 |
Ligands and binding sites
- U · Uridine-5'-monophosphate · ligand · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 283 | 0.61 | 0.79 | 42 | empty |
| 2 | 201 | 0.50 | 0.77 | 29 | empty |
| 3 | 118 | 0.43 | 0.77 | 18 | empty |
| 4 | 113 | 0.42 | 0.77 | 20 | empty |
| 5 | 117 | 0.40 | 0.74 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 4829 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 1471 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1352 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5L8Q · Structure of deformed wing virus, a honeybee pathogen · 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 L0CTV4
- Every structure of UniProt E0YTW0
- Every structure of UniProt Q7TG18
- Elsewhere: RCSB PDB 5L8Q · PDBe 5L8Q · UniProt L0CTV4 · UniProt E0YTW0 · UniProt Q7TG18
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