MolNFT v2 · #221125 · protein
Structure of the IL-5 Signaling Complex
8TLD · Cytokine receptor common subunit beta: “Structure of the IL-5 Signaling Complex”. Electron microscopy at 3.6, 1 ligand (NAG), 7 pockets (best druggability 0.78). MolNFT v2 #221125 on GenesisL1: 3D structure, binding sites and…
- PDB
- 8TLD
- Type
- protein
- Length
- 731 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.6
- Source
- Homo sapiens
- Molecule
- Cytokine receptor common subunit beta; Interleukin-5; Interleukin-5 receptor subunit alpha
- UniProt
- P32927, P05113, Q01344
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.78
Structure
electron microscopy · resolution 3.6 · 5 distinct chains · 21% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Cytokine receptor common subunit beta | protein | 94 | 10% helix, 41% strand | P32927 |
| C | Interleukin-5 | protein | 107 | 63% helix, 2% strand | P05113 |
| D | Interleukin-5 | protein | 109 | 65% helix, 3% strand | P05113 |
| E | Cytokine receptor common subunit beta | protein | 113 | 3% helix, 48% strand | P32927 |
| F | Interleukin-5 receptor subunit alpha | protein | 308 | 1% helix, 50% strand | Q01344 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1029 | 0.78 | 0.80 | 82 | empty |
| 2 | 408 | 0.63 | 0.78 | 55 | empty |
| 3 | 131 | 0.39 | 0.74 | 19 | empty |
| 4 | 62 | 0.36 | 0.78 | 15 | empty |
| 5 | 68 | 0.35 | 0.77 | 22 | empty |
Interfaces
7 interfaces between chains.
- C–D · 3419 Ų buried · 28 hydrogen bonds · protein-protein
- B–E · 1142 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 838 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 771 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 416 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- Q01344 · AlphaFold monomer V2.0 prediction for interleukin-5 receptor subunit alpha (Q01344) · a predicted model of the same protein · chain F against A, TM-score 0.98
- P32927 · AlphaFold monomer V2.0 prediction for cytokine receptor common subunit beta (P32927) · a predicted model of the same protein · chain E against A, TM-score 0.97
- P05113 · AlphaFold monomer V2.0 prediction for interleukin-5 (P05113) · a predicted model of the same protein · chain C against A, TM-score 0.92
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 P32927
- Every structure of UniProt P05113
- Every structure of UniProt Q01344
- Elsewhere: RCSB PDB 8TLD · PDBe 8TLD · UniProt P32927 · UniProt P05113 · UniProt Q01344
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