Research workbench
Structure of beta hairpin deletion mutant of beta toxin from staphylococcus aureus
Analyse Structure of beta hairpin deletion mutant of beta toxin from staphylococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K55
- Type
- protein
- Length
- 4,480 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-hemolysin
- EC
- 3.1.4.12
- UniProt
- A7LAI8
- Ligands
- NA, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P | Beta-hemolysin (EC 3.1.4.12) | protein | 280 | 19% helix, 30% strand | A7LAI8 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 817 | 0.81 | 0.84 | 93 | empty |
| 2 | 831 | 0.81 | 0.84 | 93 | NA |
| 3 | 754 | 0.78 | 0.82 | 60 | empty |
| 4 | 682 | 0.74 | 0.80 | 48 | empty |
| 5 | 841 | 0.71 | 0.76 | 83 | empty |
Interfaces
28 interfaces between chains.
- C–D · 3450 Ų buried · 70 hydrogen bonds · protein-protein
- E–F · 3447 Ų buried · 66 hydrogen bonds · protein-protein
- G–H · 3385 Ų buried · 65 hydrogen bonds · protein-protein
- A–B · 3380 Ų buried · 66 hydrogen bonds · protein-protein
- M–N · 3300 Ų buried · 63 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 3K55 · Structure of beta hairpin deletion mutant of beta toxin from Staphylococcus aureus · the same entry in another collection · chain G against G, 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 3K55 · PDBe 3K55 · UniProt A7LAI8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.