Research workbench
Structure of deformed wing virus, a honeybee pathogen
Analyse Structure of deformed wing virus, a honeybee pathogen in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MV5
- Type
- protein
- Length
- 885 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 0.64
Structure
electron microscopy · 3 distinct chains · 8% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 252 | 10% helix, 27% strand | L0CTV4 |
| B | VP2 | protein | 250 | 9% helix, 30% strand | E0YTW0 |
| C | VP3 | protein | 383 | 6% helix, 30% 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 310 | 0.64 | 0.80 | 42 | empty |
| 2 | 191 | 0.50 | 0.77 | 29 | empty |
| 3 | 177 | 0.46 | 0.75 | 22 | empty |
| 4 | 143 | 0.45 | 0.77 | 24 | empty |
| 5 | 136 | 0.45 | 0.76 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 4934 Ų buried · 69 hydrogen bonds · protein-protein
- A–B · 1496 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1357 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5MV5 · 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 5MV5 · PDBe 5MV5 · UniProt L0CTV4 · UniProt E0YTW0 · UniProt Q7TG18
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