Research workbench
Dupilumab Fab with crystal kappa design complexed with human il-4 receptor
Analyse Dupilumab Fab with crystal kappa design complexed with human il-4 receptor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WGL
- Type
- protein
- Length
- 616 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dupilumab Fab heavy chain; Dupilumab Fab light chain; Interleukin-4 receptor subunit alpha
- UniProt
- P24394
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dupilumab Fab heavy chain | protein | 222 | 7% helix, 49% strand | — |
| B | Dupilumab Fab light chain | protein | 216 | 7% helix, 54% strand | — |
| C | Interleukin-4 receptor subunit alpha | protein | 178 | 6% helix, 44% strand | P24394 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 713 | 0.66 | 0.75 | 68 | empty |
| 2 | 98 | 0.46 | 0.79 | 18 | empty |
| 3 | 105 | 0.39 | 0.75 | 17 | empty |
| 4 | 57 | 0.38 | 0.80 | 15 | empty |
| 5 | 55 | 0.28 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1851 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 698 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 309 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6WGL · Dupilumab fab with Crystal Kappa design complexed with human IL-4 receptor · the same entry in another collection · chain A against A, TM-score 1.00
- P24394 · AlphaFold monomer V2.0 prediction for interleukin-4 receptor subunit alpha (P24394) · a predicted model of the same protein · chain C against A, TM-score 0.92
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 P24394
- Elsewhere: RCSB PDB 6WGL · PDBe 6WGL · UniProt P24394
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