MolNFT v1 · #114438 · protein
Crystal structure of the water-soluble frac purified starting from the trans-membrane pore
5BPG · Fragaceatoxin C: “Crystal structure of the water-soluble frac purified starting from the trans-membrane pore”. X-ray diffraction, 1 ligand (CL), 11 pockets (best druggability 0.61). MolNFT v1 #114438 on GenesisL1: 3D structure…
- PDB
- 5BPG
- Type
- protein
- Length
- 708 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fragaceatoxin C
- UniProt
- B9W5G6
- Ligands
- CL
- Pockets
- 11 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Fragaceatoxin C | protein | 177 | 14% helix, 47% strand | B9W5G6 |
Ligands and binding sites
- CL · Chloride ion · ion · 7 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 220 | 0.61 | 0.81 | 34 | CL |
| 2 | 210 | 0.59 | 0.80 | 37 | CL |
| 3 | 140 | 0.56 | 0.82 | 25 | CL, GOL |
| 4 | 153 | 0.44 | 0.75 | 28 | GOL |
| 5 | 140 | 0.43 | 0.75 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 468 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 462 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 284 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5BPG · Crystal structure of the water-soluble FraC purified starting from the trans-membrane pore · the same entry in another collection · chain D against D, TM-score 1.00
- B9W5G6 · AlphaFold monomer V2.0 prediction for delta-actitoxin-AFR1A (B9W5G6) · a predicted model of the same protein · 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 B9W5G6
- Elsewhere: RCSB PDB 5BPG · PDBe 5BPG · UniProt B9W5G6
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