MolNFT v1 · #83658 · protein + DNA
Crystal structure of horse TLR9 in complex with inhibitory DNA4084
3WPD · Toll-like receptor 9: “Crystal structure of horse TLR9 in complex with inhibitory DNA4084”. X-ray diffraction, 2 ligands (NAG, SO4), 9 pockets (best druggability 0.54). MolNFT v1 #83658 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3WPD
- Type
- protein + DNA
- Length
- 762 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toll-like receptor 9; DNA (5'-D(*CP*CP*TP*GP*GP*AP*TP*GP*GP*G)-3')
- UniProt
- Q2EEY0
- Ligands
- NAG, SO4
- Pockets
- 9 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toll-like receptor 9 | protein | 752 | 9% helix, 16% strand | Q2EEY0 |
| C | DNA (5'-D(*CP*CP*TP*GP*GP*AP*TP*GP*GP*G)-3') | dna | 10 | — | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.54 | 0.83 | 19 | empty |
| 2 | 131 | 0.51 | 0.81 | 19 | empty |
| 3 | 58 | 0.49 | 0.86 | 18 | empty |
| 4 | 110 | 0.39 | 0.75 | 16 | empty |
| 5 | 128 | 0.38 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–C · 1008 Ų buried · 25 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
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 Q2EEY0
- Elsewhere: RCSB PDB 3WPD · PDBe 3WPD · UniProt Q2EEY0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.