MolNFT v1 · #105824 · protein
Structure of staphylococcal enterotoxin B bound to two neutralizing antibodies, 14G8 and 6D3
4RGN · Enterotoxin type B: “Structure of staphylococcal enterotoxin B bound to two neutralizing antibodies, 14G8 and 6D3”. X-ray diffraction, 20 pockets (best druggability 0.75). MolNFT v1 #105824 on GenesisL1: 3D structure, binding sites…
- PDB
- 4RGN
- Type
- protein
- Length
- 2,146 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enterotoxin type B; 14G8 heavy chain; 14G8 light chain; 6D3 heavy chain; 6D3 light chain
- UniProt
- P01552
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 11% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Enterotoxin type B | protein | 214 | 20% helix, 42% strand | P01552 |
| B, H | 14G8 heavy chain | protein | 213 | 6% helix, 51% strand | — |
| C, L | 14G8 light chain | protein | 213 | 7% helix, 51% strand | — |
| D, F | 6D3 heavy chain | protein | 210 | 6% helix, 53% strand | — |
| E, G | 6D3 light chain | protein | 220 | 6% helix, 51% strand | — |
| S | Enterotoxin type B | protein | 220 | 20% helix, 41% strand | P01552 |
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 984 | 0.75 | 0.78 | 90 | empty |
| 2 | 609 | 0.68 | 0.77 | 55 | empty |
| 3 | 599 | 0.65 | 0.75 | 54 | empty |
| 4 | 654 | 0.64 | 0.74 | 69 | empty |
| 5 | 332 | 0.63 | 0.79 | 36 | empty |
Interfaces
13 interfaces between chains.
- B–C · 1876 Ų buried · 23 hydrogen bonds · protein-protein
- H–L · 1869 Ų buried · 23 hydrogen bonds · protein-protein
- F–G · 1734 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1727 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 622 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 4RGN · Structure of Staphylococcal Enterotoxin B bound to two neutralizing antibodies, 14G8 and… · the same entry in another collection · chain G against G, TM-score 1.00
- P01552 · AlphaFold monomer V2.0 prediction for enterotoxin type B (P01552) · a predicted model of the same protein · chain A 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 4RGN · PDBe 4RGN · UniProt P01552
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