Research workbench
Crystal structure of TOXIN/ANTITOXIN complex
Analyse Crystal structure of TOXIN/ANTITOXIN complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IMF
- Type
- protein
- Length
- 295 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Protobothrops flavoviridis
- Molecule
- Cysteine-rich venom protein triflin; Small serum protein 2
- UniProt
- Q8JI39, A7VN14
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · resolution 2.3 · 2 distinct chains · 20% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cysteine-rich venom protein triflin | protein | 214 | 27% helix, 20% strand | Q8JI39 |
| B | Small serum protein 2 | protein | 81 | 0% helix, 46% strand | A7VN14 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 391 | 0.60 | 0.76 | 30 | empty |
| 2 | 313 | 0.59 | 0.77 | 43 | MES |
| 3 | 116 | 0.37 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1172 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6IMF · Crystal structure of TOXIN/ANTITOXIN complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q8JI39 · AlphaFold monomer V2.0 prediction for cysteine-rich venom protein triflin (Q8JI39) · a predicted model of the same protein · chain A against A, TM-score 0.99
- A7VN14 · AlphaFold monomer V2.0 prediction for small serum protein 2 (A7VN14) · a predicted model of the same protein · chain B against A, TM-score 0.69
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 Q8JI39
- Every structure of UniProt A7VN14
- Elsewhere: RCSB PDB 6IMF · PDBe 6IMF · UniProt Q8JI39 · UniProt A7VN14
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