MolNFT v1 · #68741 · protein
Structure of beta hairpin deletion mutant of beta toxin from staphylococcus aureus
3K55 · Beta-hemolysin: “Structure of beta hairpin deletion mutant of beta toxin from staphylococcus aureus”. X-ray diffraction, 2 ligands (NA, CL), 20 pockets (best druggability 0.81). MolNFT v1 #68741 on GenesisL1: 3D structure, binding…
- 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
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