MolNFT v1 · #120179 · protein
Crystal structure of the complex of TLR3 and bi-specific diabody
5GS0 · Toll-like receptor 3: “Crystal structure of the complex of TLR3 and bi-specific diabody”. X-ray diffraction, 3 ligands (NAG, BMA, MAN), 20 pockets (best druggability 0.73). MolNFT v1 #120179 on GenesisL1: 3D structure, binding sites…
- PDB
- 5GS0
- Type
- protein
- Length
- 2,226 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toll-like receptor 3; Light chain (anti-TLR3); Heavy chain (anti-TLR3); Heavy chain…
- UniProt
- O15455
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 7 distinct chains · 7% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Toll-like receptor 3 | protein | 663 | 10% helix, 17% strand | O15455 |
| C, E | Light chain (anti-TLR3) | protein | 107 | 6% helix, 45% strand | — |
| D, F | Heavy chain (anti-TLR3) | protein | 122 | 2% helix, 55% strand | — |
| X | Heavy chain (anti-lid) | protein | 114 | 5% helix, 54% strand | — |
| Y | Light chain (anti-lid) | protein | 107 | 0% helix, 43% strand | — |
| H | Heavy chain (anti-lid) | protein | 116 | 5% helix, 49% strand | — |
| L | Light chain (anti-lid) | protein | 105 | 0% helix, 41% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 34 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 4 copies
- MAN · alpha-D-mannopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 551 | 0.73 | 0.81 | 74 | empty |
| 2 | 573 | 0.67 | 0.77 | 55 | empty |
| 3 | 153 | 0.57 | 0.82 | 26 | empty |
| 4 | 240 | 0.47 | 0.73 | 30 | empty |
| 5 | 205 | 0.44 | 0.73 | 27 | empty |
Interfaces
11 interfaces between chains.
- A–B · 1391 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 921 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 877 Ų buried · 6 hydrogen bonds · protein-protein
- H–L · 851 Ų buried · 6 hydrogen bonds · protein-protein
- X–Y · 811 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
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 5GS0 · PDBe 5GS0 · UniProt O15455
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