Research workbench
Crystal structure of horse TLR9 in complex with two dnas (cpg DNA and tcgcac DNA)
Analyse Crystal structure of horse TLR9 in complex with two dnas (cpg DNA and tcgcac… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y3J
- Type
- protein + DNA
- Length
- 1,532 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toll-like receptor 9; DNA (5'-D(*AP*GP*GP*CP*GP*TP*TP*TP*TP*T)-3'); DNA…
- UniProt
- Q2EEY0
- Ligands
- NAG, MG
- Pockets
- 16 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Toll-like receptor 9 | protein | 750 | 11% helix, 16% strand | Q2EEY0 |
| C, D | DNA (5'-D(*AP*GP*GP*CP*GP*TP*TP*TP*TP*T)-3') | dna | 10 | — | — |
| E, F | DNA (5'-D(*TP*CP*GP*CP*AP*C)-3') | dna | 6 | — | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 461 | 0.64 | 0.77 | 48 | empty |
| 2 | 103 | 0.54 | 0.84 | 17 | empty |
| 3 | 102 | 0.54 | 0.83 | 22 | empty |
| 4 | 253 | 0.49 | 0.74 | 34 | empty |
| 5 | 214 | 0.45 | 0.74 | 26 | empty |
Interfaces
5 interfaces between chains.
- B–D · 996 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–C · 993 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–B · 628 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 501 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–F · 499 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 17 glycan, 14 disulfide (N-glycosylation, disulfide).
Compared structures
- 5Y3J · Crystal structure of horse TLR9 in complex with two DNAs (CpG DNA and TCGCAC DNA) · the same entry in another collection · chain C against C, TM-score 1.00
- Q2EEY0 · AlphaFold monomer V2.0 prediction for toll-like receptor 9 (Q2EEY0) · 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 Q2EEY0
- Elsewhere: RCSB PDB 5Y3J · PDBe 5Y3J · UniProt Q2EEY0
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