MolNFT v1 · #140218 · protein + DNA
Crystal structure of bovine TLR9 in complex with two dnas (cpg DNA and tcgttt DNA)
5Y3M · Toll-like receptor 9: “Crystal structure of bovine TLR9 in complex with two dnas (cpg DNA and tcgttt DNA)”. X-ray diffraction, 1 ligand (NAG), 14 pockets (best druggability 0.69). MolNFT v1 #140218 on GenesisL1: 3D structure…
- PDB
- 5Y3M
- Type
- protein + DNA
- Length
- 1,491 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toll-like receptor 9; DNA (5'-D(*TP*CP*GP*T)-3'); DNA (5'-D(P*GP*GP*CP*GP*TP*T)-3')
- UniProt
- Q5I2M5
- Ligands
- NAG
- Pockets
- 14 · best druggability 0.69
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toll-like receptor 9 | protein | 738 | 11% helix, 17% strand | Q5I2M5 |
| E | DNA (5'-D(*TP*CP*GP*T)-3') | dna | 4 | — | — |
| F | DNA (5'-D(*TP*CP*GP*T)-3') | dna | 5 | — | — |
| D, C | DNA (5'-D(P*GP*GP*CP*GP*TP*T)-3') | dna | 6 | — | — |
| B | Toll-like receptor 9 | protein | 732 | 12% helix, 17% strand | Q5I2M5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, F, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 553 | 0.69 | 0.78 | 50 | empty |
| 2 | 423 | 0.68 | 0.80 | 39 | empty |
| 3 | 255 | 0.58 | 0.79 | 25 | empty |
| 4 | 95 | 0.49 | 0.81 | 16 | empty |
| 5 | 93 | 0.45 | 0.80 | 18 | empty |
Interfaces
9 interfaces between chains.
- A–B · 2163 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 722 Ų buried · 13 hydrogen bonds · protein-nucleic
- D–B · 692 Ų buried · 11 hydrogen bonds · protein-nucleic
- F–B · 550 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–E · 493 Ų buried · 10 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 14 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 5Y3M · Crystal structure of bovine TLR9 in complex with two DNAs (CpG DNA and TCGTTT DNA) · the same entry in another collection · chain B against B, TM-score 1.00
- Q5I2M5 · AlphaFold monomer V2.0 prediction for toll-like receptor 9 (Q5I2M5) · 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 Q5I2M5
- Elsewhere: RCSB PDB 5Y3M · PDBe 5Y3M · UniProt Q5I2M5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.