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Crystal structure of frac with dhpc bound (crystal form III)
Analyse Crystal structure of frac with dhpc bound (crystal form III) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TSQ
- Type
- protein
- Length
- 1,065 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fragaceatoxin C
- UniProt
- B9W5G6
- Ligands
- HXG, PC, SCN, CL
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, F | Fragaceatoxin C | protein | 177 | 14% helix, 47% strand | B9W5G6 |
| B, D, E | Fragaceatoxin C | protein | 178 | 13% helix, 47% strand | B9W5G6 |
Ligands and binding sites
- HXG · 1,2-dihexanoyl-sn-glycero-3-phosphocholine · ligand · 16 copies · chains A, E, B, C, D, F
- PC · Phosphocholine · ligand · 8 copies · chains A, C, D, E, F
- SCN · Thiocyanate ion · ion · 5 copies · chains A, B, D, E, F
- CL · Chloride ion · ion · 2 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 878 | 0.81 | 0.84 | 100 | HXG |
| 2 | 316 | 0.68 | 0.82 | 42 | empty |
| 3 | 148 | 0.57 | 0.83 | 26 | empty |
| 4 | 92 | 0.54 | 0.84 | 19 | empty |
| 5 | 181 | 0.54 | 0.79 | 39 | SCN |
Interfaces
10 interfaces between chains.
- D–E · 523 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 515 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 512 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 406 Ų buried · 3 hydrogen bonds · protein-protein
- C–E · 376 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
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 4TSQ · PDBe 4TSQ · UniProt B9W5G6
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