MolNFT v1 · #129921 · protein
Sacbrood virus of honeybee
5OYP · Structural protein VP1: “Sacbrood virus of honeybee”. Electron microscopy, 10 pockets (best druggability 0.66). MolNFT v1 #129921 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5OYP
- Type
- protein
- Length
- 781 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Structural protein VP1; Structural protein VP2; Structural protein VP3; Minor capsid…
- UniProt
- A0A223DN69, Q6ITS8, Q9IGK7
- Pockets
- 10 · best druggability 0.66
Structure
electron microscopy · 4 distinct chains · 10% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Structural protein VP1 | protein | 243 | 13% helix, 34% strand | A0A223DN69 |
| B | Structural protein VP2 | protein | 239 | 11% helix, 42% strand | Q6ITS8 |
| C | Structural protein VP3 | protein | 273 | 7% helix, 30% strand | A0A223DN69 |
| D | Minor capsid protein micp | protein | 26 | 0% helix, 8% strand | Q9IGK7 |
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 393 | 0.66 | 0.80 | 38 | empty |
| 2 | 53 | 0.60 | 0.92 | 15 | empty |
| 3 | 59 | 0.51 | 0.87 | 18 | empty |
| 4 | 91 | 0.45 | 0.80 | 19 | empty |
| 5 | 141 | 0.44 | 0.76 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–C · 5526 Ų buried · 59 hydrogen bonds · protein-protein
- A–B · 1430 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1363 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 668 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 363 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5OYP · Sacbrood virus of honeybee · 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 A0A223DN69
- Every structure of UniProt Q6ITS8
- Every structure of UniProt Q9IGK7
- Elsewhere: RCSB PDB 5OYP · PDBe 5OYP · UniProt A0A223DN69 · UniProt Q6ITS8 · UniProt Q9IGK7
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