Research workbench
Crystal structure of beta toxin 275-280 from staphylococcus aureus
Analyse Crystal structure of beta toxin 275-280 from staphylococcus aureus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3I5V
- Type
- protein
- Length
- 1,139 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-hemolysin
- UniProt
- A7LAI8
- Ligands
- DGA
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Beta-hemolysin | protein | 285 | 20% helix, 29% strand | A7LAI8 |
| C | Beta-hemolysin | protein | 284 | 20% helix, 29% strand | A7LAI8 |
Ligands and binding sites
- DGA · Diacyl glycerol · ligand · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1191 | 0.79 | 0.81 | 120 | empty |
| 2 | 862 | 0.76 | 0.80 | 76 | empty |
| 3 | 955 | 0.74 | 0.77 | 79 | empty |
| 4 | 441 | 0.68 | 0.80 | 33 | empty |
| 5 | 452 | 0.67 | 0.79 | 34 | empty |
Interfaces
5 interfaces between chains.
- A–D · 744 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 504 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 466 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 309 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 182 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 3I5V · Crystal structure of beta toxin 275-280 from Staphylococcus aureus · 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 A7LAI8
- Elsewhere: RCSB PDB 3I5V · PDBe 3I5V · UniProt A7LAI8
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