Research workbench
Native virion of kashmir bee virus at neutral pH
Analyse Native virion of kashmir bee virus at neutral pH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BGK
- Type
- protein
- Length
- 814 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Structural polyprotein
- UniProt
- Q6SQI6, Q80AG2
- Pockets
- 8 · best druggability 0.71
Structure
electron microscopy · 4 distinct chains · 11% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Structural polyprotein | protein | 58 | 17% helix, 2% strand | Q6SQI6 |
| A | Structural polyprotein | protein | 208 | 18% helix, 30% strand | Q80AG2 |
| C | Structural polyprotein | protein | 298 | 7% helix, 32% strand | Q80AG2 |
| B | Structural polyprotein | protein | 250 | 10% helix, 35% strand | Q80AG2 |
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 761 | 0.71 | 0.78 | 61 | empty |
| 2 | 173 | 0.62 | 0.84 | 34 | empty |
| 3 | 51 | 0.55 | 0.90 | 16 | empty |
| 4 | 210 | 0.48 | 0.74 | 28 | empty |
| 5 | 132 | 0.42 | 0.75 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–C · 4725 Ų buried · 72 hydrogen bonds · protein-protein
- C–B · 1585 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1202 Ų buried · 24 hydrogen bonds · protein-protein
- D–C · 1012 Ų buried · 10 hydrogen bonds · protein-protein
- D–A · 215 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7BGK · Native virion of Kashmir bee virus at neutral pH · the same entry in another collection · chain D against D, 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 Q6SQI6
- Every structure of UniProt Q80AG2
- Elsewhere: RCSB PDB 7BGK · PDBe 7BGK · UniProt Q6SQI6 · UniProt Q80AG2
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