MolNFT v1 · #81276 · protein
Structure of quaternary complex of human TLR3ECD with three fabs (FORM1)
3ULU · Toll-like receptor 3: “Structure of quaternary complex of human TLR3ECD with three fabs (FORM1)”. X-ray diffraction, 4 ligands (NAG, BMA, MAN), 20 pockets (best druggability 0.67). MolNFT v1 #81276 on GenesisL1: 3D structure…
- PDB
- 3ULU
- Type
- protein
- Length
- 1,964 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toll-like receptor 3; FAB15 light chain; FAB15 heavy chain; FAB12 light chain; FAB12…
- UniProt
- O15455
- Ligands
- NAG, BMA, MAN, SO4
- Pockets
- 20 · best druggability 0.67
Structure
x-ray diffraction · 7 distinct chains · 6% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toll-like receptor 3 | protein | 659 | 10% helix, 17% strand | O15455 |
| L | FAB15 light chain | protein | 214 | 4% helix, 50% strand | — |
| H | FAB15 heavy chain | protein | 225 | 1% helix, 51% strand | — |
| C | FAB12 light chain | protein | 210 | 7% helix, 47% strand | — |
| D | FAB12 heavy chain | protein | 224 | 4% helix, 50% strand | — |
| E | FAB1068 light chain | protein | 215 | 4% helix, 49% strand | — |
| F | FAB1068 heavy chain | protein | 217 | 3% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains A, E
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar · chains L
- SO4 · Sulfate ion · ion · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 698 | 0.67 | 0.75 | 59 | empty |
| 2 | 91 | 0.53 | 0.84 | 17 | empty |
| 3 | 239 | 0.53 | 0.76 | 33 | empty |
| 4 | 344 | 0.52 | 0.73 | 41 | empty |
| 5 | 179 | 0.51 | 0.78 | 31 | empty |
Interfaces
9 interfaces between chains.
- L–H · 2106 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1977 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1956 Ų buried · 14 hydrogen bonds · protein-protein
- A–H · 753 Ų buried · 13 hydrogen bonds · protein-protein
- A–F · 648 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 11 glycan (disulfide, N-glycosylation).
Compared structures
- 3ULU · Structure of quaternary complex of human TLR3ecd with three Fabs (Form1) · the same entry in another collection · chain F against F, TM-score 1.00
- O15455 · AlphaFold monomer V2.0 prediction for toll-like receptor 3 (O15455) · 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 O15455
- Elsewhere: RCSB PDB 3ULU · PDBe 3ULU · UniProt O15455
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