Research workbench
Structure of C-terminal fragment of VIP3A toxin
Analyse Structure of C-terminal fragment of VIP3A toxin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VLS
- Type
- protein
- Length
- 3,820 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MALTOSE/MALTODEXTRIN-binding periplasmic PROTEIN,VIP3AA
- UniProt
- P0AEX9, W8GI72
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MALTOSE/MALTODEXTRIN-binding periplasmic PROTEIN,VIP3AA | protein | 953 | 29% helix, 32% strand | P0AEX9, W8GI72 |
| B | MALTOSE/MALTODEXTRIN-binding periplasmic PROTEIN,VIP3AA | protein | 950 | 29% helix, 32% strand | P0AEX9, W8GI72 |
| C | MALTOSE/MALTODEXTRIN-binding periplasmic PROTEIN,VIP3AA | protein | 954 | 29% helix, 32% strand | P0AEX9, W8GI72 |
| D | MALTOSE/MALTODEXTRIN-binding periplasmic PROTEIN,VIP3AA | protein | 963 | 28% helix, 32% strand | P0AEX9, W8GI72 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 848 | 0.76 | 0.79 | 66 | PEG |
| 2 | 417 | 0.72 | 0.83 | 40 | empty |
| 3 | 949 | 0.72 | 0.76 | 80 | PEG |
| 4 | 1073 | 0.71 | 0.75 | 106 | PEG |
| 5 | 711 | 0.71 | 0.78 | 51 | PEG |
Interfaces
3 interfaces between chains.
- A–B · 3702 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 3617 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 480 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6VLS · Structure of C-terminal fragment of Vip3A toxin · 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 P0AEX9
- Every structure of UniProt W8GI72
- Elsewhere: RCSB PDB 6VLS · PDBe 6VLS · UniProt P0AEX9 · UniProt W8GI72
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