MolNFT v1 · #158202 · protein
A cytokine-receptor complex
6NMY · Interleukin-3 receptor subunit alpha: “A cytokine-receptor complex”. X-ray diffraction, 3 ligands (NAG, BMA, FUC), 20 pockets (best druggability 0.79). MolNFT v1 #158202 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6NMY
- Type
- protein
- Length
- 1,571 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-3 receptor subunit alpha; Cytokine receptor common subunit beta; Interleukin-3
- UniProt
- P26951, P32927, P08700
- Ligands
- NAG, BMA, FUC
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 9% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | Interleukin-3 receptor subunit alpha | protein | 270 | 3% helix, 48% strand | P26951 |
| M | Interleukin-3 receptor subunit alpha | protein | 262 | 3% helix, 49% strand | P26951 |
| A, C | Cytokine receptor common subunit beta | protein | 215 | 6% helix, 42% strand | P32927 |
| I, J | Interleukin-3 | protein | 108 | 61% helix, 0% strand | P08700 |
| B | Cytokine receptor common subunit beta | protein | 196 | 5% helix, 48% strand | P32927 |
| D | Cytokine receptor common subunit beta | protein | 197 | 5% helix, 51% strand | P32927 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains F, M, A, C
- BMA · beta-D-mannopyranose · sugar · 5 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 830 | 0.79 | 0.82 | 83 | empty |
| 2 | 64 | 0.71 | 0.97 | 18 | empty |
| 3 | 716 | 0.67 | 0.76 | 73 | empty |
| 4 | 148 | 0.66 | 0.87 | 32 | empty |
| 5 | 411 | 0.63 | 0.78 | 55 | empty |
Interfaces
17 interfaces between chains.
- C–D · 2665 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 2630 Ų buried · 43 hydrogen bonds · protein-protein
- F–J · 1256 Ų buried · 20 hydrogen bonds · protein-protein
- M–I · 1220 Ų buried · 17 hydrogen bonds · protein-protein
- F–B · 914 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 6NMY · A Cytokine-receptor complex · the same entry in another collection · chain D against D, TM-score 1.00
- P32927 · AlphaFold monomer V2.0 prediction for cytokine receptor common subunit beta (P32927) · a predicted model of the same protein · chain D against A, TM-score 0.97
- P26951 · AlphaFold monomer V2.0 prediction for interleukin-3 receptor subunit alpha (P26951) · a predicted model of the same protein · chain M 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 P26951
- Every structure of UniProt P32927
- Every structure of UniProt P08700
- Elsewhere: RCSB PDB 6NMY · PDBe 6NMY · UniProt P26951 · UniProt P32927 · UniProt P08700
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