Research workbench
Structure of quaternary complex of human TLR3ECD with three fabs (FORM2)
Analyse Structure of quaternary complex of human TLR3ECD with three fabs (FORM2) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ULV
- Type
- protein
- Length
- 1,973 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 0.68
Structure
x-ray diffraction · 7 distinct chains · 5% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toll-like receptor 3 | protein | 668 | 10% helix, 18% strand | O15455 |
| L | FAB15 light chain | protein | 214 | 4% helix, 49% strand | — |
| H | FAB15 heavy chain | protein | 225 | 1% helix, 51% strand | — |
| C | FAB12 light chain | protein | 210 | 6% helix, 47% strand | — |
| D | FAB12 heavy chain | protein | 224 | 3% helix, 48% strand | — |
| E | FAB1068 light chain | protein | 215 | 2% helix, 51% strand | — |
| F | FAB1068 heavy chain | protein | 217 | 3% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, E
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
- SO4 · Sulfate ion · ion · 6 copies · chains A, L, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.68 | 0.95 | 18 | empty |
| 2 | 702 | 0.65 | 0.74 | 63 | empty |
| 3 | 513 | 0.60 | 0.74 | 66 | empty |
| 4 | 87 | 0.56 | 0.87 | 22 | empty |
| 5 | 436 | 0.56 | 0.73 | 54 | empty |
Interfaces
9 interfaces between chains.
- L–H · 2115 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1901 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1806 Ų buried · 14 hydrogen bonds · protein-protein
- A–H · 774 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 621 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 11 glycan (disulfide, N-glycosylation).
Compared structures
- 3ULV · Structure of quaternary complex of human TLR3ecd with three Fabs (Form2) · 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 3ULV · PDBe 3ULV · UniProt O15455
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