Research workbench
Structure of a cytokine ligand-receptor complex
Analyse Structure of a cytokine ligand-receptor complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QT2
- Type
- protein
- Length
- 1,051 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-5 receptor subunit alpha; Interleukin-5
- UniProt
- Q01344, P05113
- Ligands
- BGC
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 25% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-5 receptor subunit alpha | protein | 307 | 3% helix, 52% strand | Q01344 |
| C | Interleukin-5 | protein | 110 | 68% helix, 5% strand | P05113 |
| D, F | Interleukin-5 | protein | 109 | 65% helix, 4% strand | P05113 |
| B | Interleukin-5 receptor subunit alpha | protein | 307 | 3% helix, 51% strand | Q01344 |
| E | Interleukin-5 | protein | 109 | 68% helix, 6% strand | P05113 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 6 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 774 | 0.77 | 0.81 | 61 | empty |
| 2 | 774 | 0.76 | 0.81 | 67 | empty |
| 3 | 405 | 0.71 | 0.82 | 37 | empty |
| 4 | 369 | 0.70 | 0.82 | 42 | empty |
| 5 | 61 | 0.40 | 0.80 | 13 | empty |
Interfaces
7 interfaces between chains.
- E–F · 3575 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 3494 Ų buried · 29 hydrogen bonds · protein-protein
- B–E · 865 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 825 Ų buried · 19 hydrogen bonds · protein-protein
- B–F · 539 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 3QT2 · Structure of a cytokine ligand-receptor complex · the same entry in another collection · chain D against D, TM-score 1.00
- Q01344 · AlphaFold monomer V2.0 prediction for interleukin-5 receptor subunit alpha (Q01344) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P05113 · AlphaFold monomer V2.0 prediction for interleukin-5 (P05113) · a predicted model of the same protein · chain D 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 Q01344
- Every structure of UniProt P05113
- Elsewhere: RCSB PDB 3QT2 · PDBe 3QT2 · UniProt Q01344 · UniProt P05113
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