MolNFT v1 · #105503 · protein
Il-18 receptor complex
4R6U · Interleukin-18 receptor 1: “Il-18 receptor complex”. X-ray diffraction, 1 ligand (NAG), 7 pockets (best druggability 0.83). MolNFT v1 #105503 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4R6U
- Type
- protein
- Length
- 859 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-18 receptor 1; Interleukin-18
- UniProt
- Q13478, Q14116
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Interleukin-18 receptor 1 | protein | 275 | 4% helix, 53% strand | Q13478 |
| A | Interleukin-18 receptor 1 | protein | 274 | 4% helix, 53% strand | Q13478 |
| B, D | Interleukin-18 | protein | 155 | 8% helix, 52% strand | Q14116 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains C, B, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 791 | 0.83 | 0.86 | 82 | empty |
| 2 | 1116 | 0.82 | 0.83 | 103 | empty |
| 3 | 122 | 0.59 | 0.85 | 19 | empty |
| 4 | 100 | 0.46 | 0.80 | 23 | empty |
| 5 | 51 | 0.35 | 0.80 | 16 | empty |
Interfaces
5 interfaces between chains.
- C–B · 1589 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 1562 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 265 Ų buried · 5 hydrogen bonds · protein-protein
- C–A · 174 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 79 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 4R6U · IL-18 receptor complex · the same entry in another collection · chain C against C, TM-score 1.00
- Q14116 · AlphaFold monomer V2.0 prediction for interleukin-18 (Q14116) · a predicted model of the same protein · chain B 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 C against A, TM-score 0.95
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 Q13478
- Every structure of UniProt Q14116
- Elsewhere: RCSB PDB 4R6U · PDBe 4R6U · UniProt Q13478 · UniProt Q14116
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