Research workbench
Crystal structure of horse TLR9 in complex with agonistic DNA1668_12MER
Analyse Crystal structure of horse TLR9 in complex with agonistic DNA1668_12MER in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WPC
- Type
- protein + DNA
- Length
- 1,520 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toll-like receptor 9; DNA (5'-D(*CP*AP*TP*GP*AP*CP*GP*TP*TP*CP*CP*T)-3')
- UniProt
- Q2EEY0
- Ligands
- NAG, NA, SO4
- Pockets
- 16 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toll-like receptor 9 | protein | 747 | 11% helix, 16% strand | Q2EEY0 |
| B | Toll-like receptor 9 | protein | 749 | 11% helix, 16% strand | Q2EEY0 |
| F, E | DNA (5'-D(*CP*AP*TP*GP*AP*CP*GP*TP*TP*CP*CP*T)-3') | dna | 12 | — | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains A, B, F, E
- NA · Sodium ion · metal · chains B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1036 | 0.71 | 0.75 | 103 | empty |
| 2 | 309 | 0.69 | 0.84 | 35 | empty |
| 3 | 285 | 0.69 | 0.84 | 34 | empty |
| 4 | 386 | 0.66 | 0.80 | 44 | empty |
| 5 | 371 | 0.62 | 0.78 | 43 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2145 Ų buried · 16 hydrogen bonds · protein-protein
- B–F · 1113 Ų buried · 26 hydrogen bonds · protein-nucleic
- A–E · 1113 Ų buried · 29 hydrogen bonds · protein-nucleic
- B–E · 275 Ų buried · 4 hydrogen bonds · protein-nucleic
- A–F · 271 Ų buried · 2 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 15 glycan, 14 disulfide (N-glycosylation, disulfide).
Compared structures
- 3WPC · Crystal structure of horse TLR9 in complex with agonistic DNA1668_12mer · the same entry in another collection · chain A against A, TM-score 1.00
- Q2EEY0 · AlphaFold monomer V2.0 prediction for toll-like receptor 9 (Q2EEY0) · a predicted model of the same protein · chain B 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 Q2EEY0
- Elsewhere: RCSB PDB 3WPC · PDBe 3WPC · UniProt Q2EEY0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.