Research workbench
Crystal structure of the pore forming toxin frac from sea anemone actinia fragacea
Analyse Crystal structure of the pore forming toxin frac from sea anemone actinia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LIM
- Type
- protein
- Length
- 1,068 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fragaceatoxin C
- UniProt
- B9W5G6
- Pockets
- 17 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Fragaceatoxin C | protein | 178 | 13% helix, 47% strand | B9W5G6 |
Ligands and binding sites
- LDA · Lauryl dimethylamine-N-oxide · additive · 18 copies · chains A, E, B, D, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 303 | 0.52 | 0.74 | 54 | empty |
| 2 | 117 | 0.43 | 0.77 | 24 | empty |
| 3 | 98 | 0.41 | 0.77 | 20 | empty |
| 4 | 105 | 0.41 | 0.77 | 22 | empty |
| 5 | 164 | 0.40 | 0.73 | 26 | empty |
Interfaces
9 interfaces between chains.
- A–B · 664 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 629 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 622 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 620 Ų buried · 8 hydrogen bonds · protein-protein
- A–F · 168 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3LIM · Crystal structure of the pore forming toxin frac from sea anemone actinia fragacea · the same entry in another collection · chain F against F, TM-score 1.00
- B9W5G6 · AlphaFold monomer V2.0 prediction for delta-actitoxin-AFR1A (B9W5G6) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 B9W5G6
- Elsewhere: RCSB PDB 3LIM · PDBe 3LIM · UniProt B9W5G6
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