Research workbench
Crystal structure of mouse TLR9 in complex with inhibitory DNA_SUPER
Analyse Crystal structure of mouse TLR9 in complex with inhibitory DNA_SUPER in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WPI
- Type
- protein + DNA
- Length
- 736 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*CP*AP*AP*TP*AP*GP*GP*GP*TP*GP*AP*GP*GP*GP*G)-3'…
- UniProt
- Q9EQU3
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toll-like receptor 9 | protein | 727 | 10% helix, 17% strand | Q9EQU3 |
| B | DNA (5'- D(*CP*CP*TP*CP*AP*AP*TP*AP*GP*GP*GP*TP*GP*AP*GP*GP*GP*G)-3') | dna | 9 | — | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 273 | 0.63 | 0.81 | 45 | empty |
| 2 | 86 | 0.56 | 0.86 | 23 | empty |
| 3 | 59 | 0.39 | 0.81 | 13 | empty |
| 4 | 59 | 0.34 | 0.77 | 13 | empty |
| 5 | 66 | 0.34 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 814 Ų buried · 22 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3WPI · Crystal structure of mouse TLR9 in complex with inhibitory DNA_super · 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 3WPI · PDBe 3WPI · UniProt Q9EQU3
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