Research workbench
Pore forming toxin
Analyse Pore forming toxin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P24
- Type
- protein
- Length
- 2,039 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-hemolysin
- UniProt
- Q99UU6
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Alpha-hemolysin | protein | 292 | 4% helix, 59% strand | Q99UU6 |
| B, C, E | Alpha-hemolysin | protein | 291 | 4% helix, 60% strand | Q99UU6 |
| D | Alpha-hemolysin | protein | 292 | 5% helix, 60% strand | Q99UU6 |
| F | Alpha-hemolysin | protein | 290 | 4% helix, 59% strand | Q99UU6 |
Ligands and binding sites
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 13 copies · chains A, F, G, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 352 | 0.71 | 0.83 | 45 | MPD |
| 2 | 354 | 0.70 | 0.83 | 54 | empty |
| 3 | 576 | 0.69 | 0.78 | 81 | MPD |
| 4 | 280 | 0.67 | 0.83 | 45 | MPD |
| 5 | 494 | 0.67 | 0.78 | 59 | MPD |
Interfaces
14 interfaces between chains.
- B–C · 2975 Ų buried · 60 hydrogen bonds · protein-protein
- A–B · 2952 Ų buried · 61 hydrogen bonds · protein-protein
- F–G · 2949 Ų buried · 65 hydrogen bonds · protein-protein
- C–D · 2948 Ų buried · 69 hydrogen bonds · protein-protein
- E–F · 2935 Ų buried · 61 hydrogen bonds · protein-protein
Compared structures
- 4P24 · pore forming toxin · the same entry in another collection · 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 Q99UU6
- Elsewhere: RCSB PDB 4P24 · PDBe 4P24 · UniProt Q99UU6
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