Research workbench
Crystal structure of the IL4-IL4R-common gamma ternary complex
Analyse Crystal structure of the IL4-IL4R-common gamma ternary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BPL
- Type
- protein
- Length
- 522 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-4; Interleukin-4 receptor alpha chain; Cytokine receptor common gamma chain
- UniProt
- P05112, P24394, P31785
- Ligands
- NAG, FUC
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-4 | protein | 126 | 61% helix, 5% strand | P05112 |
| B | Interleukin-4 receptor alpha chain | protein | 202 | 8% helix, 46% strand | P24394 |
| C | Cytokine receptor common gamma chain | protein | 194 | 6% helix, 47% strand | P31785 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains B, C
- FUC · alpha-L-fucopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 235 | 0.58 | 0.80 | 35 | empty |
| 2 | 124 | 0.56 | 0.83 | 19 | empty |
| 3 | 229 | 0.52 | 0.77 | 37 | empty |
| 4 | 176 | 0.48 | 0.76 | 26 | empty |
| 5 | 110 | 0.40 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 833 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 739 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 570 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 3BPL · Crystal structure of the IL4-IL4R-Common Gamma ternary complex · the same entry in another collection · chain A against A, TM-score 1.00
- P31785 · AlphaFold monomer V2.0 prediction for cytokine receptor common subunit gamma (P31785) · a predicted model of the same protein · chain C against A, TM-score 0.98
- P24394 · AlphaFold monomer V2.0 prediction for interleukin-4 receptor subunit alpha (P24394) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P05112 · AlphaFold monomer V2.0 prediction for interleukin-4 (P05112) · a predicted model of the same protein · chain A 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 P05112
- Every structure of UniProt P24394
- Every structure of UniProt P31785
- Elsewhere: RCSB PDB 3BPL · PDBe 3BPL · UniProt P05112 · UniProt P24394 · UniProt P31785
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