Research workbench
Mouse toll-like receptor 3 ectodomain complexed with double-stranded RNA
Analyse Mouse toll-like receptor 3 ectodomain complexed with double-stranded RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CIY
- Type
- protein + RNA
- Length
- 1,421 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 46-mer; Toll-like receptor 3
- UniProt
- Q99MB1
- Ligands
- NAG, NDG, MAN, BMA, FUC, FUL
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 46-mer | rna | 46 | — | — |
| D | 46-mer | rna | 46 | — | — |
| A | Toll-like receptor 3 | protein | 661 | 9% helix, 18% strand | Q99MB1 |
| B | Toll-like receptor 3 | protein | 668 | 9% helix, 18% strand | Q99MB1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 25 copies · chains A, B
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 7 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 7 copies · chains C, D
- BMA · beta-D-mannopyranose · sugar · 3 copies
- FUC · alpha-L-fucopyranose · sugar · chains A
- FUL · beta-L-fucopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.72 | 0.97 | 27 | empty |
| 2 | 109 | 0.71 | 0.92 | 38 | empty |
| 3 | 345 | 0.60 | 0.78 | 29 | empty |
| 4 | 186 | 0.54 | 0.79 | 39 | empty |
| 5 | 211 | 0.49 | 0.76 | 24 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2153 Ų buried · 194 hydrogen bonds · nucleic-nucleic
- A–B · 632 Ų buried · 11 hydrogen bonds · protein-protein
- D–A · 627 Ų buried · 16 hydrogen bonds · protein-nucleic
- C–A · 608 Ų buried · 6 hydrogen bonds · protein-nucleic
- D–B · 588 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 18 glycan, 8 disulfide (N-glycosylation, disulfide).
Compared structures
- 3CIY · Mouse Toll-like receptor 3 ectodomain complexed with double-stranded RNA · the same entry in another collection · chain B against B, TM-score 1.00
- Q99MB1 · AlphaFold monomer V2.0 prediction for toll-like receptor 3 (Q99MB1) · a predicted model of the same protein · chain B 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 Q99MB1
- Elsewhere: RCSB PDB 3CIY · PDBe 3CIY · UniProt Q99MB1
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