MolNFT v1 · #140215 · protein + DNA
Crystal structure of horse TLR9 in complex with two dnas (cpg DNA and tcgcac DNA)
5Y3J · Toll-like receptor 9: “Crystal structure of horse TLR9 in complex with two dnas (cpg DNA and tcgcac DNA)”. X-ray diffraction, 2 ligands (NAG, MG), 16 pockets (best druggability 0.64). MolNFT v1 #140215 on GenesisL1: 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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