Research workbench
Sacbrood virus of honeybee - expansion state I
Analyse Sacbrood virus of honeybee - expansion state I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EGX
- Type
- protein
- Length
- 727 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
- A0A223DN59, A0A223DN66, A0A2I6HDZ6, Q9IGK7
- Pockets
- 9 · best druggability 0.58
Structure
electron microscopy · 4 distinct chains · 10% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Structural protein VP1 | protein | 229 | 12% helix, 35% strand | A0A223DN59 |
| B | Structural protein VP2 | protein | 199 | 11% helix, 44% strand | A0A223DN66 |
| C | Structural protein VP3 | protein | 273 | 8% helix, 30% strand | A0A2I6HDZ6 |
| D | Minor capsid protein micp | protein | 26 | 0% helix, 8% strand | Q9IGK7 |
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 | 68 | 0.58 | 0.89 | 22 | empty |
| 2 | 59 | 0.51 | 0.87 | 18 | empty |
| 3 | 102 | 0.46 | 0.80 | 19 | empty |
| 4 | 122 | 0.44 | 0.77 | 19 | empty |
| 5 | 120 | 0.40 | 0.75 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–C · 5013 Ų buried · 55 hydrogen bonds · protein-protein
- B–C · 1262 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1106 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 682 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 347 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6EGX · Sacbrood virus of honeybee - expansion state I · 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 A0A223DN59
- Every structure of UniProt A0A223DN66
- Every structure of UniProt A0A2I6HDZ6
- Every structure of UniProt Q9IGK7
- Elsewhere: RCSB PDB 6EGX · PDBe 6EGX · UniProt A0A223DN59 · UniProt A0A223DN66 · UniProt A0A2I6HDZ6 · UniProt Q9IGK7
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