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Crystal structure of the unliganded human interleukin-7 receptor extracellular domain
Analyse Crystal structure of the unliganded human interleukin-7 receptor extracellular… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UP1
- Type
- protein
- Length
- 397 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-7 receptor subunit alpha
- UniProt
- P16871
- Ligands
- NAG, FUC, NGA, SO4
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-7 receptor subunit alpha | protein | 201 | 7% helix, 53% strand | P16871 |
| B | Interleukin-7 receptor subunit alpha | protein | 196 | 5% helix, 53% strand | P16871 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · chains B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.72 | 0.97 | 16 | NGA |
| 2 | 193 | 0.52 | 0.77 | 24 | empty |
| 3 | 67 | 0.42 | 0.81 | 15 | GOL |
Interfaces
1 interface between chains.
- A–B · 611 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation, O-glycosylation).
Compared structures
- 3UP1 · Crystal structure of the unliganded human interleukin-7 receptor extracellular domain · the same entry in another collection · chain A against A, TM-score 1.00
- P16871 · AlphaFold monomer V2.0 prediction for interleukin-7 receptor subunit alpha (P16871) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P16871
- Elsewhere: RCSB PDB 3UP1 · PDBe 3UP1 · UniProt P16871
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