MolNFT v1 · #67955 · protein
Homology model of human toll-like receptor 5 fitted into an electron microscopy single particle reconstruction
3J0A: “Homology model of human toll-like receptor 5 fitted into an electron microscopy single particle reconstruction”. Electron microscopy, 2 ligands (NAG, FUC), 20 pockets (best druggability 0.86). MolNFT v1 #67955 on GenesisL1: 3D…
- PDB
- 3J0A
- Type
- protein
- Length
- 1,429 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toll-like receptor 5
- UniProt
- O60602
- Ligands
- NAG, FUC
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 2 distinct chains · 12% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toll-like receptor 5 | protein | 797 | 13% helix, 16% strand | O60602 |
| B | Toll-like receptor 5 | protein | 632 | 10% helix, 16% strand | O60602 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 14 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.86 | 0.95 | 57 | empty |
| 2 | 99 | 0.78 | 0.97 | 24 | empty |
| 3 | 153 | 0.77 | 0.94 | 22 | empty |
| 4 | 99 | 0.77 | 0.96 | 24 | empty |
| 5 | 98 | 0.76 | 0.96 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 754 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 3J0A · Homology model of human Toll-like receptor 5 fitted into an electron microscopy single… · the same entry in another collection · chain A against A, TM-score 1.00
- O60602 · AlphaFold monomer V2.0 prediction for toll-like receptor 5 (O60602) · a predicted model of the same protein · chain B against A, TM-score 0.77
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 O60602
- Elsewhere: RCSB PDB 3J0A · PDBe 3J0A · UniProt O60602
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.