Research workbench
Crystal structure of the il-18 signaling ternary complex
Analyse Crystal structure of the il-18 signaling ternary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WO4
- Type
- protein
- Length
- 728 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-18; Interleukin-18 receptor 1; Interleukin-18 receptor accessory protein
- UniProt
- Q14116, Q13478, O95256
- Ligands
- NAG, BMA, MAN, FUC, CL
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-18 | protein | 157 | 8% helix, 52% strand | Q14116 |
| B | Interleukin-18 receptor 1 | protein | 301 | 3% helix, 49% strand | Q13478 |
| C | Interleukin-18 receptor accessory protein | protein | 270 | 4% helix, 49% strand | O95256 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains B, A, C
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains B
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains B, A
- CL · Chloride ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1020 | 0.85 | 0.86 | 86 | empty |
| 2 | 185 | 0.69 | 0.87 | 36 | CL |
| 3 | 203 | 0.63 | 0.83 | 35 | empty |
| 4 | 255 | 0.54 | 0.76 | 39 | empty |
| 5 | 147 | 0.46 | 0.77 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1762 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 844 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 420 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 glycan, 9 disulfide (N-glycosylation, disulfide).
Compared structures
- 3WO4 · Crystal structure of the IL-18 signaling ternary complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q14116 · AlphaFold monomer V2.0 prediction for interleukin-18 (Q14116) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q13478 · AlphaFold monomer V2.0 prediction for interleukin-18 receptor 1 (Q13478) · a predicted model of the same protein · chain B against A, TM-score 0.97
- O95256 · AlphaFold monomer V2.0 prediction for interleukin-18 receptor accessory protein (O95256) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 Q14116
- Every structure of UniProt Q13478
- Every structure of UniProt O95256
- Elsewhere: RCSB PDB 3WO4 · PDBe 3WO4 · UniProt Q14116 · UniProt Q13478 · UniProt O95256
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