MolNFT v1 · #105823 · protein
Structure of staphylococcal enterotoxin B bound to the neutralizing antibody 20B1
4RGM · Enterotoxin type B: “Structure of staphylococcal enterotoxin B bound to the neutralizing antibody 20B1”. X-ray diffraction, 17 pockets (best druggability 0.54). MolNFT v1 #105823 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4RGM
- Type
- protein
- Length
- 1,306 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enterotoxin type B; 20B1 light chain; 20B1 heavy chain
- UniProt
- P01552
- Pockets
- 17 · best druggability 0.54
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| S | Enterotoxin type B | protein | 224 | 19% helix, 40% strand | P01552 |
| L, B | 20B1 light chain | protein | 213 | 6% helix, 51% strand | — |
| H | 20B1 heavy chain | protein | 216 | 8% helix, 53% strand | — |
| A | Enterotoxin type B | protein | 223 | 19% helix, 39% strand | P01552 |
| C | 20B1 heavy chain | protein | 217 | 7% helix, 51% strand | — |
Pockets
17 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 347 | 0.54 | 0.74 | 48 | empty |
| 2 | 326 | 0.52 | 0.74 | 36 | empty |
| 3 | 106 | 0.51 | 0.82 | 16 | empty |
| 4 | 108 | 0.50 | 0.81 | 18 | empty |
| 5 | 258 | 0.49 | 0.74 | 39 | empty |
Interfaces
7 interfaces between chains.
- L–H · 1868 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1862 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 849 Ų buried · 8 hydrogen bonds · protein-protein
- S–H · 792 Ų buried · 8 hydrogen bonds · protein-protein
- H–C · 238 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 4RGM · Structure of Staphylococcal Enterotoxin B bound to the neutralizing antibody 20B1 · the same entry in another collection · chain C against C, 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 4RGM · PDBe 4RGM · UniProt P01552
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