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Structure of the AhlB pore of the tripartite alpha-pore forming toxin, AHL, from Aeromonas hydrophila.
Analyse Structure of the AhlB pore of the tripartite alpha-pore forming toxin, AHL… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GRJ
- Type
- protein
- Length
- 3,285 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.94
- Source
- Aeromonas hydrophila
- Molecule
- AhlB
- UniProt
- A0A081US78
- Ligands
- NA, CL, PO4
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · resolution 2.94 · 7 distinct chains · 89% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, A, C | AhlB | protein | 338 | 88% helix, 0% strand | A0A081US78 |
| J, B | AhlB | protein | 322 | 88% helix, 0% strand | A0A081US78 |
| D | AhlB | protein | 320 | 88% helix, 0% strand | A0A081US78 |
| E | AhlB | protein | 338 | 88% helix, 0% strand | A0A081US78 |
| F | AhlB | protein | 317 | 89% helix, 0% strand | A0A081US78 |
| H | AhlB | protein | 337 | 89% helix, 0% strand | A0A081US78 |
| I | AhlB | protein | 315 | 90% helix, 0% strand | A0A081US78 |
Ligands and binding sites
- NA · Sodium ion · metal · 10 copies · chains J, A, B, C, D, E, F, H, I
- CL · Chloride ion · ion · 27 copies · chains G, J, A, B, C, D, E, F, H, I
- PO4 · Phosphate ion · ion · 2 copies · chains G, J, E
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 14 copies · chains G, I, J, C, A, F, E, D, H, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 990 | 0.71 | 0.75 | 91 | MPD |
| 2 | 901 | 0.69 | 0.75 | 85 | MPD |
| 3 | 888 | 0.69 | 0.75 | 94 | CL, MPD |
| 4 | 840 | 0.69 | 0.75 | 80 | MPD |
| 5 | 724 | 0.66 | 0.75 | 67 | MPD |
Interfaces
10 interfaces between chains.
- C–D · 2925 Ų buried · 39 hydrogen bonds · protein-protein
- E–F · 2911 Ų buried · 36 hydrogen bonds · protein-protein
- H–I · 2899 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 2897 Ų buried · 38 hydrogen bonds · protein-protein
- G–J · 2852 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 50 modified (engineered).
Compared structures
- 6GRJ · Structure of the ahlb pore of the tripartite alpha-pore forming toxin, ahl, from… · 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 A0A081US78
- Elsewhere: RCSB PDB 6GRJ · PDBe 6GRJ · UniProt A0A081US78
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