Research workbench
VIP3AA toxin structure
Analyse VIP3AA toxin structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TFK
- Type
- protein
- Length
- 2,724 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vegetative insecticidal protein
- UniProt
- Q58XI2
- Ligands
- MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 1 distinct chain · 29% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Vegetative insecticidal protein | protein | 681 | 29% helix, 33% strand | Q58XI2 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 812 | 0.83 | 0.86 | 75 | empty |
| 2 | 254 | 0.54 | 0.76 | 35 | empty |
| 3 | 247 | 0.51 | 0.75 | 29 | empty |
| 4 | 204 | 0.50 | 0.76 | 25 | empty |
| 5 | 196 | 0.48 | 0.75 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2767 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 2752 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 2750 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 2747 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 207 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6TFK · Vip3Aa toxin structure · 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 Q58XI2
- Elsewhere: RCSB PDB 6TFK · PDBe 6TFK · UniProt Q58XI2
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