Research workbench
Vip3Bc1 tetramer in processed, activated state
Analyse Vip3Bc1 tetramer in processed, activated state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YRG
- Type
- protein
- Length
- 2,736 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.8
- Source
- Bacillus thuringiensis
- Molecule
- Vegetative insecticidal protein
- UniProt
- A0A290WPI2
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · resolution 4.8 · 1 distinct chain · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Vegetative insecticidal protein | protein | 684 | 29% helix, 28% strand | A0A290WPI2 |
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 709 | 0.83 | 0.87 | 69 | empty |
| 2 | 142 | 0.82 | 0.98 | 36 | empty |
| 3 | 146 | 0.82 | 0.98 | 37 | empty |
| 4 | 104 | 0.71 | 0.93 | 22 | empty |
| 5 | 108 | 0.70 | 0.92 | 25 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2873 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2858 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 2853 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 2850 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 218 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6YRG · VIP3BC1 tetramer in processed, activated state · 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 A0A290WPI2
- Elsewhere: RCSB PDB 6YRG · PDBe 6YRG · UniProt A0A290WPI2
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