Research workbench
Structural basis of cytosolic DNA recognition by innate immune receptors
Analyse Structural basis of cytosolic DNA recognition 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
- 3RN5
- Type
- protein + DNA
- Length
- 851 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interferon-inducible protein AIM2; DNA (5'- D(*CP*CP*AP*TP*CP*AP*AP*AP*GP*AP*GP*AP*GP*AP*A…
- UniProt
- O14862
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Interferon-inducible protein AIM2 | protein | 194 | 11% helix, 49% strand | O14862 |
| D | Interferon-inducible protein AIM2 | protein | 193 | 10% helix, 51% strand | O14862 |
| K, M | DNA (5'- D(*CP*CP*AP*TP*CP*AP*AP*AP*GP*AP*GP*AP*GP*AP*AP*AP*GP*AP*G)-3') | dna | 19 | — | — |
| L, N | DNA (5'- D(*GP*CP*TP*CP*TP*TP*TP*CP*TP*CP*TP*CP*TP*TP*TP*GP*AP*TP*G)-3') | dna | 19 | — | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 531 | 0.78 | 0.85 | 57 | empty |
| 2 | 409 | 0.77 | 0.87 | 48 | EDO |
| 3 | 472 | 0.77 | 0.85 | 61 | EDO |
| 4 | 384 | 0.76 | 0.86 | 47 | EDO |
| 5 | 124 | 0.50 | 0.80 | 20 | empty |
Interfaces
16 interfaces between chains.
- M–N · 814 Ų buried · 85 hydrogen bonds · nucleic-nucleic
- K–L · 804 Ų buried · 85 hydrogen bonds · nucleic-nucleic
- A–D · 441 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 404 Ų buried · 7 hydrogen bonds · protein-protein
- C–N · 355 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 3RN5 · Structural basis of cytosolic DNA recognition by innate immune receptors · the same entry in another collection · chain N against N, TM-score 1.00
- O14862 · AlphaFold monomer V2.0 prediction for interferon-inducible protein AIM2 (O14862) · a predicted model of the same protein · chain C 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 O14862
- Elsewhere: RCSB PDB 3RN5 · PDBe 3RN5 · UniProt O14862
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