Research workbench
Crystal structure of the N-terminal domain of drosophila toll receptor with the magic triangle I3C
Analyse Crystal structure of the N-terminal domain of drosophila toll receptor with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ARR
- Type
- protein
- Length
- 544 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toll receptor, variable lymphocyte receptor B.61 chimera
- UniProt
- P08953, Q4G1L2
- Ligands
- I3C, NAG
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Toll receptor, variable lymphocyte receptor B.61 chimera | protein | 272 | 14% helix, 22% strand | P08953, Q4G1L2 |
Ligands and binding sites
- I3C · 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 353 | 0.64 | 0.79 | 36 | I3C |
| 2 | 305 | 0.59 | 0.78 | 54 | empty |
| 3 | 136 | 0.44 | 0.76 | 18 | empty |
| 4 | 85 | 0.35 | 0.75 | 17 | empty |
| 5 | 73 | 0.34 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1227 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 4ARR · Crystal structure of the N-terminal domain of Drosophila Toll receptor with the magic… · 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 0.90
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 Q4G1L2
- Elsewhere: RCSB PDB 4ARR · PDBe 4ARR · UniProt P08953 · UniProt Q4G1L2
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