MolNFT v1 · #82938 · protein
Crystal structure of staphylococcal eenterotoxin B in complex with a novel neutralization monoclonal antibody Fab fragment
3W2D · Enterotoxin type B: “Crystal structure of staphylococcal eenterotoxin B in complex with a novel neutralization monoclonal antibody…”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.46). MolNFT v1 #82938 on…
- PDB
- 3W2D
- Type
- protein
- Length
- 663 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enterotoxin type B; Monoclonal antibody 3E2 Fab figment light chain; Monoclonal antibody…
- UniProt
- P01552
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.46
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Enterotoxin type B | protein | 225 | 14% helix, 32% strand | P01552 |
| L | Monoclonal antibody 3E2 Fab figment light chain | protein | 215 | 7% helix, 43% strand | — |
| H | Monoclonal antibody 3E2 Fab figment heavy chain | protein | 223 | 3% helix, 49% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 151 | 0.46 | 0.77 | 29 | empty |
| 2 | 71 | 0.46 | 0.83 | 18 | empty |
| 3 | 170 | 0.45 | 0.75 | 29 | empty |
| 4 | 139 | 0.43 | 0.76 | 26 | empty |
| 5 | 182 | 0.41 | 0.73 | 23 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1995 Ų buried · 19 hydrogen bonds · protein-protein
- A–H · 563 Ų buried · 11 hydrogen bonds · protein-protein
- A–L · 381 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 3W2D · Crystal Structure of Staphylococcal Eenterotoxin B in complex with a novel neutralization… · the same entry in another collection · chain A against A, 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 0.98
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 3W2D · PDBe 3W2D · UniProt P01552
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