MolNFT v1 · #159912 · protein
Crystal structure of a complex of human il-7RALPHA with an anti-il- 7RALPHA Fab 4A10
6P50 · Interleukin-7 receptor subunit alpha: “Crystal structure of a complex of human il-7RALPHA with an anti-il- 7RALPHA Fab 4A10”. X-ray diffraction, 1 ligand (NAG), 7 pockets (best druggability 0.52). MolNFT v1 #159912 on GenesisL1: 3D…
- PDB
- 6P50
- Type
- protein
- Length
- 522 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-7 receptor subunit alpha; Anti-il-7R 4A10 Fab heavy chain; Anti-il-7R 4A10…
- UniProt
- P16871
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Interleukin-7 receptor subunit alpha | protein | 90 | 0% helix, 54% strand | P16871 |
| H | Anti-il-7R 4A10 Fab heavy chain | protein | 221 | 5% helix, 48% strand | — |
| L | Anti-il-7R 4A10 Fab light chain | protein | 211 | 5% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 353 | 0.52 | 0.73 | 46 | empty |
| 2 | 221 | 0.48 | 0.74 | 34 | empty |
| 3 | 113 | 0.45 | 0.78 | 21 | empty |
| 4 | 65 | 0.37 | 0.79 | 15 | empty |
| 5 | 96 | 0.37 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1706 Ų buried · 12 hydrogen bonds · protein-protein
- C–H · 546 Ų buried · 9 hydrogen bonds · protein-protein
- C–L · 123 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6P50 · Crystal Structure of a Complex of human IL-7Ralpha with an anti-IL-7Ralpha Fab 4A10 · the same entry in another collection · chain H against H, 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 C against A, TM-score 0.93
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 6P50 · PDBe 6P50 · UniProt P16871
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