Research workbench
Crystal structure of il-18 in complex with il-18 receptor alpha
Analyse Crystal structure of il-18 in complex with il-18 receptor alpha in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WO3
- Type
- protein
- Length
- 2,624 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-18; Interleukin-18 receptor 1
- UniProt
- Q14116, Q13478
- Ligands
- NAG, BMA, MAN, FUC, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 8 distinct chains · 4% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G, I, K | Interleukin-18 | protein | 156 | 8% helix, 55% strand | Q14116 |
| B | Interleukin-18 receptor 1 | protein | 294 | 3% helix, 52% strand | Q13478 |
| D | Interleukin-18 receptor 1 | protein | 290 | 3% helix, 53% strand | Q13478 |
| E | Interleukin-18 | protein | 157 | 6% helix, 55% strand | Q14116 |
| F | Interleukin-18 receptor 1 | protein | 288 | 3% helix, 52% strand | Q13478 |
| H | Interleukin-18 receptor 1 | protein | 288 | 3% helix, 53% strand | Q13478 |
| J | Interleukin-18 receptor 1 | protein | 272 | 3% helix, 46% strand | Q13478 |
| L | Interleukin-18 receptor 1 | protein | 255 | 2% helix, 50% strand | Q13478 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 59 copies · chains B, A, H, D, C, F, E, J, G, I, L, K
- BMA · beta-D-mannopyranose · sugar · 17 copies · chains B, D, E, F, J, H, A, L
- MAN · alpha-D-mannopyranose · sugar · 12 copies · chains D, H, B, F, C, J
- FUC · alpha-L-fucopyranose · sugar · 8 copies · chains B, A, D, C, E, F, G, H, I, J, K, L
- SO4 · Sulfate ion · ion · 38 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1132 | 0.83 | 0.84 | 90 | SO4 |
| 2 | 1104 | 0.82 | 0.83 | 95 | SO4 |
| 3 | 1176 | 0.82 | 0.83 | 89 | SO4 |
| 4 | 1130 | 0.81 | 0.82 | 103 | SO4 |
| 5 | 1109 | 0.81 | 0.82 | 93 | SO4 |
Interfaces
19 interfaces between chains.
- C–D · 1781 Ų buried · 36 hydrogen bonds · protein-protein
- G–H · 1757 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 1755 Ų buried · 36 hydrogen bonds · protein-protein
- E–F · 1739 Ų buried · 31 hydrogen bonds · protein-protein
- I–J · 1643 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 glycan, 30 disulfide (N-glycosylation, disulfide).
Compared structures
- 3WO3 · Crystal structure of IL-18 in complex with IL-18 receptor alpha · the same entry in another collection · chain L against L, 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 Q14116
- Every structure of UniProt Q13478
- Elsewhere: RCSB PDB 3WO3 · PDBe 3WO3 · UniProt Q14116 · UniProt Q13478
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