MolNFT v1 · #127390 · protein
Structure of deformed wing virus, a honeybee pathogen
5MV6 · VP1: “Structure of deformed wing virus, a honeybee pathogen”. Electron microscopy, 1 ligand (U), 9 pockets (best druggability 0.71). MolNFT v1 #127390 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5MV6
- Type
- protein
- Length
- 860 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 0.71
Structure
electron microscopy · 3 distinct chains · 10% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 240 | 11% helix, 23% strand | L0CTV4 |
| B | VP2 | protein | 249 | 13% helix, 30% strand | E0YTW0 |
| C | VP3 | protein | 371 | 8% helix, 26% 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.71 | 0.94 | 21 | empty |
| 2 | 434 | 0.65 | 0.78 | 70 | empty |
| 3 | 121 | 0.57 | 0.83 | 26 | empty |
| 4 | 66 | 0.55 | 0.87 | 21 | empty |
| 5 | 220 | 0.52 | 0.77 | 35 | empty |
Interfaces
3 interfaces between chains.
- A–C · 4760 Ų buried · 73 hydrogen bonds · protein-protein
- A–B · 1444 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1420 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5MV6 · 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 5MV6 · PDBe 5MV6 · UniProt L0CTV4 · UniProt E0YTW0 · UniProt Q7TG18
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