MolNFT v1 · #99244 · protein
Structure of the toll - spatzle complex, a molecular hub in drosophila development and innate immunity (glycosylated form)
4LXS · Protein toll: “Structure of the toll - spatzle complex, a molecular hub in drosophila development and innate immunity…”. X-ray diffraction, 3 ligands (NAG, BMA, MAN), 5 pockets (best druggability 0.74). MolNFT v1 #99244 on…
- PDB
- 4LXS
- Type
- protein
- Length
- 875 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein toll; Protein spaetzle C-106
- UniProt
- P08953, P48607
- Ligands
- NAG, BMA, MAN
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein toll | protein | 747 | 12% helix, 19% strand | P08953 |
| J | Protein spaetzle C-106 | protein | 63 | 0% helix, 43% strand | P48607 |
| K | Protein spaetzle C-106 | protein | 65 | 0% helix, 40% strand | P48607 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 copies · chains A, J, K
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains J, A
- MAN · alpha-D-mannopyranose · sugar · chains J
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 661 | 0.74 | 0.81 | 66 | empty |
| 2 | 477 | 0.65 | 0.77 | 57 | empty |
| 3 | 97 | 0.36 | 0.75 | 22 | empty |
| 4 | 58 | 0.35 | 0.78 | 15 | empty |
| 5 | 78 | 0.34 | 0.75 | 19 | empty |
Interfaces
3 interfaces between chains.
- J–K · 1506 Ų buried · 16 hydrogen bonds · protein-protein
- A–K · 1160 Ų buried · 19 hydrogen bonds · protein-protein
- A–J · 723 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 4LXS · Structure of the Toll - Spatzle complex, a molecular hub in Drosophila development and… · the same entry in another collection · chain A against A, TM-score 1.00
- P08953 · AlphaFold monomer V2.0 prediction for protein toll (P08953) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P48607 · AlphaFold monomer V2.0 prediction for protein spaetzle (P48607) · a predicted model of the same protein · chain J against A, TM-score 0.89
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 P08953
- Every structure of UniProt P48607
- Elsewhere: RCSB PDB 4LXS · PDBe 4LXS · UniProt P08953 · UniProt P48607
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