Research workbench
De novo structure of the binary mosquito larvicide binab at pH 10
Analyse De novo structure of the binary mosquito larvicide binab at pH 10 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FOZ
- Type
- protein
- Length
- 783 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toxin; Larvicidal toxin protein
- UniProt
- P06575, P10565
- Ligands
- NA
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toxin | protein | 364 | 12% helix, 45% strand | P06575 |
| B | Larvicidal toxin protein | protein | 419 | 12% helix, 42% strand | P10565 |
Ligands and binding sites
- NA · Sodium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1154 | 0.77 | 0.79 | 98 | empty |
| 2 | 1093 | 0.76 | 0.78 | 105 | empty |
| 3 | 108 | 0.44 | 0.78 | 23 | empty |
| 4 | 70 | 0.36 | 0.77 | 18 | empty |
| 5 | 66 | 0.32 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1894 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5FOZ · De novo structure of the binary mosquito larvicide BinAB at pH 10 · the same entry in another collection · chain A against A, TM-score 1.00
- P06575 · AlphaFold monomer V2.0 prediction for binary larvicide subunit bina (P06575) · a predicted model of the same protein · chain A against A, TM-score 0.94
- P10565 · AlphaFold monomer V2.0 prediction for binary larvicide subunit binb (P10565) · a predicted model of the same protein · chain B against A, TM-score 0.89
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 P06575
- Every structure of UniProt P10565
- Elsewhere: RCSB PDB 5FOZ · PDBe 5FOZ · UniProt P06575 · UniProt P10565
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