Research workbench
Crystal structure of ternary complex of il-24 with soluble receptors il-22RA and il-20RB
Analyse Crystal structure of ternary complex of il-24 with soluble receptors il-22RA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DF3
- Type
- protein
- Length
- 544 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-22 receptor subunit alpha-1; Interleukin-24; Interleukin-20 receptor subunit…
- UniProt
- Q8N6P7, Q13007, Q6UXL0
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Interleukin-22 receptor subunit alpha-1 | protein | 199 | 6% helix, 50% strand | Q8N6P7 |
| C | Interleukin-24 | protein | 155 | 71% helix, 6% strand | Q13007 |
| H | Interleukin-20 receptor subunit beta | protein | 190 | 6% helix, 44% strand | Q6UXL0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains L, C
- GOL · Glycerol · additive · 2 copies · chains L, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 280 | 0.64 | 0.81 | 37 | empty |
| 2 | 457 | 0.60 | 0.75 | 41 | empty |
| 3 | 158 | 0.51 | 0.78 | 34 | empty |
| 4 | 91 | 0.37 | 0.76 | 15 | empty |
| 5 | 59 | 0.31 | 0.76 | 13 | empty |
Interfaces
3 interfaces between chains.
- L–C · 1020 Ų buried · 22 hydrogen bonds · protein-protein
- C–H · 929 Ų buried · 15 hydrogen bonds · protein-protein
- L–H · 471 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6DF3 · Crystal structure of ternary complex of IL-24 with soluble receptors IL-22RA and IL-20RB · the same entry in another collection · chain L against L, TM-score 1.00
- Q13007 · AlphaFold monomer V2.0 prediction for interleukin-24 (Q13007) · a predicted model of the same protein · chain C against A, TM-score 0.99
- Q8N6P7 · AlphaFold monomer V2.0 prediction for interleukin-22 receptor subunit alpha-1 (Q8N6P7) · a predicted model of the same protein · chain L against A, TM-score 0.98
- Q6UXL0 · AlphaFold monomer V2.0 prediction for interleukin-20 receptor subunit beta (Q6UXL0) · a predicted model of the same protein · chain H 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 Q8N6P7
- Every structure of UniProt Q13007
- Every structure of UniProt Q6UXL0
- Elsewhere: RCSB PDB 6DF3 · PDBe 6DF3 · UniProt Q8N6P7 · UniProt Q13007 · UniProt Q6UXL0
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