MolNFT v1 · #141867 · protein + DNA
Crystal structure of mouse TLR9 in complex with two dnas (cpg DNA and tcgcca DNA)
5ZLN · Toll-like receptor 9: “Crystal structure of mouse TLR9 in complex with two dnas (cpg DNA and tcgcca DNA)”. X-ray diffraction, 3 ligands (NAG, BMA, SO4), 20 pockets (best druggability 0.71). MolNFT v1 #141867 on GenesisL1: 3D…
- PDB
- 5ZLN
- 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
- Q9EQU3
- Ligands
- NAG, BMA, SO4
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toll-like receptor 9 | protein | 751 | 12% helix, 16% strand | Q9EQU3 |
| B | Toll-like receptor 9 | protein | 753 | 13% helix, 16% strand | Q9EQU3 |
| 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*C)-3') | dna | 4 | — | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 25 copies · chains A, F, D, B, E, C
- BMA · beta-D-mannopyranose · sugar · 2 copies
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.71 | 0.81 | 56 | empty |
| 2 | 188 | 0.67 | 0.86 | 26 | empty |
| 3 | 255 | 0.65 | 0.83 | 39 | empty |
| 4 | 175 | 0.65 | 0.86 | 28 | empty |
| 5 | 631 | 0.64 | 0.75 | 65 | empty |
Interfaces
9 interfaces between chains.
- A–B · 2071 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 987 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–C · 960 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–E · 465 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–F · 441 Ų buried · 9 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 16 disulfide, 14 glycan (disulfide, N-glycosylation).
Compared structures
- 5ZLN · Crystal structure of mouse TLR9 in complex with two DNAs (CpG DNA and TCGCCA DNA) · the same entry in another collection · chain F against F, TM-score 1.00
- Q9EQU3 · AlphaFold monomer V2.0 prediction for toll-like receptor 9 (Q9EQU3) · a predicted model of the same protein · chain B against A, TM-score 1.00
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 Q9EQU3
- Elsewhere: RCSB PDB 5ZLN · PDBe 5ZLN · UniProt Q9EQU3
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