Research workbench
Pore structure of pore-forming toxin EPX4
Analyse Pore structure of pore-forming toxin EPX4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7T4D
- Type
- protein
- Length
- 602 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- EPX4
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 62% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | EPX4 | protein | 301 | 4% helix, 62% strand | — |
Ligands and binding sites
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.65 | 0.86 | 31 | empty |
| 2 | 312 | 0.58 | 0.77 | 40 | empty |
| 3 | 86 | 0.39 | 0.77 | 16 | empty |
| 4 | 113 | 0.35 | 0.73 | 26 | empty |
| 5 | 68 | 0.31 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- B–A · 2932 Ų buried · 69 hydrogen bonds · protein-protein
Compared structures
- 7T4D · Pore structure of pore-forming toxin Epx4 · the same entry in another collection · chain B against B, 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
- Elsewhere: RCSB PDB 7T4D · PDBe 7T4D
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