MolNFT v1 · #166821 · protein
VIP3B (VIP3B_2160) adapted for crystallization
6V1V · Vegetative insecticidal protein: “VIP3B (VIP3B_2160) adapted for crystallization”. X-ray diffraction, 20 pockets (best druggability 0.86). MolNFT v1 #166821 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6V1V
- Type
- protein
- Length
- 2,972 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vegetative insecticidal protein
- UniProt
- A0A290WPI2
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vegetative insecticidal protein | protein | 752 | 34% helix, 32% strand | A0A290WPI2 |
| B | Vegetative insecticidal protein | protein | 750 | 33% helix, 32% strand | A0A290WPI2 |
| C | Vegetative insecticidal protein | protein | 739 | 33% helix, 33% strand | A0A290WPI2 |
| D | Vegetative insecticidal protein | protein | 731 | 34% helix, 32% strand | A0A290WPI2 |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 736 | 0.86 | 0.90 | 84 | empty |
| 2 | 194 | 0.82 | 0.96 | 30 | empty |
| 3 | 156 | 0.80 | 0.96 | 26 | empty |
| 4 | 944 | 0.77 | 0.79 | 101 | empty |
| 5 | 744 | 0.76 | 0.80 | 72 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2562 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 2554 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1466 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1327 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 647 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6V1V · VIP3B (VIP3B_2160) adapted for crystallization · 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 6V1V · PDBe 6V1V · UniProt A0A290WPI2
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