Research workbench
Denmotoxin: a the three-finger toxin from colubrid snake boiga dendrophila with bird-specific activity
Analyse Denmotoxin: a the three-finger toxin from colubrid snake boiga dendrophila with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2H5F
- Type
- protein
- Length
- 149 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Denmotoxin
- UniProt
- P83490
- Ligands
- K, NA, PO4
- Pockets
- 2 · best druggability 0.35
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Denmotoxin | protein | 75 | 0% helix, 44% strand | P83490 |
| B | Denmotoxin | protein | 74 | 0% helix, 47% strand | P83490 |
Ligands and binding sites
- K · Potassium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.35 | 0.75 | 17 | empty |
| 2 | 84 | 0.35 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 219 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 2H5F · Denmotoxin: A the three-finger toxin from colubrid snake Boiga dendrophila with… · the same entry in another collection · chain A against A, TM-score 1.00
- P83490 · AlphaFold monomer V2.0 prediction for alpha-colubritoxin (P83490) · a predicted model of the same protein · chain B against A, TM-score 0.85
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 P83490
- Elsewhere: RCSB PDB 2H5F · PDBe 2H5F · UniProt P83490
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