Research workbench
Crystal structure of bovine TLR9 in complex with two dnas (cpg DNA and tcgttt DNA)
Analyse Crystal structure of bovine TLR9 in complex with two dnas (cpg DNA and tcgttt… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 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.