Research workbench
Domain 4 of the beta common chain in complex with an antibody
Analyse Domain 4 of the beta common chain in complex with an antibody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EGJ
- Type
- protein
- Length
- 536 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytokine receptor common beta chain precursor; Antibody (light chain); Antibody (heavy…
- UniProt
- P32927, P01865
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytokine receptor common beta chain precursor | protein | 101 | 0% helix, 51% strand | P32927 |
| L | Antibody (light chain) | protein | 215 | 4% helix, 53% strand | — |
| H | Antibody (heavy chain) | protein | 220 | 7% helix, 49% strand | P01865 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 549 | 0.61 | 0.74 | 54 | empty |
| 2 | 193 | 0.53 | 0.78 | 22 | empty |
| 3 | 59 | 0.46 | 0.84 | 19 | empty |
| 4 | 95 | 0.44 | 0.79 | 22 | empty |
| 5 | 54 | 0.37 | 0.80 | 15 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1789 Ų buried · 19 hydrogen bonds · protein-protein
- A–H · 435 Ų buried · 5 hydrogen bonds · protein-protein
- A–L · 397 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 1EGJ · Domain 4 of the beta common chain in complex with an antibody · the same entry in another collection · chain A against A, 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 A against A, TM-score 0.91
- P01865 · AlphaFold monomer V2.0 prediction for ig gamma-2A chain C region, membrane-bound form… · a predicted model of the same protein · chain H against A, TM-score 0.52
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 P01865
- Elsewhere: RCSB PDB 1EGJ · PDBe 1EGJ · UniProt P32927 · UniProt P01865
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