MolNFT v1 · #83662 · protein + DNA
Crystal structure of mouse TLR9 in complex with inhibitory DNA4084 (form 2)
3WPH · Toll-like receptor 9: “Crystal structure of mouse TLR9 in complex with inhibitory DNA4084 (form 2)”. X-ray diffraction, 2 ligands (NAG, SO4), 5 pockets (best druggability 0.60). MolNFT v1 #83662 on GenesisL1: 3D structure, binding…
- PDB
- 3WPH
- Type
- protein + DNA
- Length
- 737 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*GP*AP*A)-3')
- UniProt
- Q9EQU3
- Ligands
- NAG, SO4
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toll-like receptor 9 | protein | 725 | 11% helix, 16% strand | Q9EQU3 |
| B | DNA (5'-D(*CP*CP*TP*GP*GP*AP*TP*GP*GP*GP*AP*A)-3') | dna | 12 | — | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.60 | 0.89 | 14 | SO4 |
| 2 | 71 | 0.58 | 0.89 | 18 | empty |
| 3 | 122 | 0.50 | 0.80 | 24 | empty |
| 4 | 89 | 0.34 | 0.74 | 18 | empty |
| 5 | 52 | 0.31 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1253 Ų buried · 34 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3WPH · Crystal structure of mouse TLR9 in complex with inhibitory DNA4084 (form 2) · the same entry in another collection · chain A against A, TM-score 1.00
- Q9EQU3 · AlphaFold monomer V2.0 prediction for toll-like receptor 9 (Q9EQU3) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9EQU3
- Elsewhere: RCSB PDB 3WPH · PDBe 3WPH · UniProt Q9EQU3
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