MolNFT v1 · #105825 · protein
Structure of staphylococcal enterotoxin B bound to the neutralizing antibody 14G8
4RGO · Enterotoxin type B: “Structure of staphylococcal enterotoxin B bound to the neutralizing antibody 14G8”. X-ray diffraction, 7 pockets (best druggability 0.64). MolNFT v1 #105825 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4RGO
- Type
- protein
- Length
- 650 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enterotoxin type B; 14G8 heavy chain; 14G8 light chain
- UniProt
- P01552
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| S | Enterotoxin type B | protein | 225 | 18% helix, 40% strand | P01552 |
| H | 14G8 heavy chain | protein | 213 | 8% helix, 51% strand | — |
| L | 14G8 light chain | protein | 212 | 6% helix, 50% strand | — |
Ligands and binding sites
- ACT · Acetate ion · additive · chains S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 592 | 0.64 | 0.75 | 54 | empty |
| 2 | 181 | 0.59 | 0.82 | 27 | empty |
| 3 | 52 | 0.51 | 0.88 | 22 | empty |
| 4 | 189 | 0.47 | 0.75 | 29 | empty |
| 5 | 64 | 0.34 | 0.77 | 16 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1848 Ų buried · 20 hydrogen bonds · protein-protein
- S–H · 649 Ų buried · 9 hydrogen bonds · protein-protein
- S–L · 404 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4RGO · Structure of Staphylococcal Enterotoxin B bound to the neutralizing antibody 14G8 · the same entry in another collection · chain S against S, TM-score 1.00
- P01552 · AlphaFold monomer V2.0 prediction for enterotoxin type B (P01552) · a predicted model of the same protein · chain S against A, TM-score 0.99
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 P01552
- Elsewhere: RCSB PDB 4RGO · PDBe 4RGO · UniProt P01552
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