Research workbench
Structural basis of cytosolic DNA sensing by innate immune receptors
Analyse Structural basis of cytosolic DNA sensing by innate immune receptors in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RNU
- Type
- protein + DNA
- Length
- 830 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-interferon-inducible protein 16; DNA (5'-D(*GP*CP*CP*AP*TP*CP*AP*AP*AP*GP*AP*GP*AP*G…
- UniProt
- Q16666
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Gamma-interferon-inducible protein 16 | protein | 199 | 10% helix, 49% strand | Q16666 |
| B | Gamma-interferon-inducible protein 16 | protein | 201 | 10% helix, 46% strand | Q16666 |
| K | DNA (5'-D(*GP*CP*CP*AP*TP*CP*AP*AP*AP*GP*AP*GP*AP*GP*AP*G)- 3') | dna | 16 | — | — |
| L | DNA (5'-D(*TP*CP*TP*CP*TP*CP*TP*TP*TP*GP*AP*TP*GP*GP*CP*C)- 3') | dna | 16 | — | — |
Ligands and binding sites
- FMT · Formic acid · additive · 5 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 545 | 0.78 | 0.85 | 47 | FMT |
| 2 | 356 | 0.71 | 0.84 | 40 | empty |
| 3 | 311 | 0.71 | 0.85 | 44 | empty |
| 4 | 380 | 0.69 | 0.82 | 37 | empty |
| 5 | 378 | 0.69 | 0.82 | 41 | empty |
Interfaces
12 interfaces between chains.
- A–D · 920 Ų buried · 12 hydrogen bonds · protein-protein
- K–L · 716 Ų buried · 71 hydrogen bonds · nucleic-nucleic
- B–K · 286 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–L · 196 Ų buried · 3 hydrogen bonds · protein-nucleic
- D–K · 169 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 3RNU · Structural Basis of Cytosolic DNA Sensing by Innate Immune Receptors · the same entry in another collection · chain L against L, TM-score 1.00
- Q16666 · AlphaFold monomer V2.0 prediction for gamma-interferon-inducible protein 16 (Q16666) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q16666
- Elsewhere: RCSB PDB 3RNU · PDBe 3RNU · UniProt Q16666
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