MolNFT v1 · #159105 · protein
Engineered Fab bound to il-4 receptor
6OEL · Engineered interleukin-4, rga variant: “Engineered Fab bound to il-4 receptor”. X-ray diffraction, 3 ligands (NAG, FUC, NO3), 12 pockets (best druggability 0.64). MolNFT v1 #159105 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6OEL
- Type
- protein
- Length
- 922 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Engineered interleukin-4, rga variant; Interleukin-4 receptor subunit alpha; Cytokine…
- UniProt
- P05112, P24394, P31785
- Ligands
- NAG, FUC, NO3
- Pockets
- 12 · best druggability 0.64
Structure
x-ray diffraction · 5 distinct chains · 13% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Engineered interleukin-4, rga variant | protein | 127 | 61% helix, 5% strand | P05112 |
| B | Interleukin-4 receptor subunit alpha | protein | 199 | 8% helix, 48% strand | P24394 |
| C | Cytokine receptor common subunit gamma | protein | 160 | 0% helix, 37% strand | P31785 |
| H | Engineered Fab heavy chain | protein | 223 | 5% helix, 55% strand | — |
| L | Engineered Fab light chain | protein | 213 | 6% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B, C
- FUC · alpha-L-fucopyranose · sugar · chains B
- NO3 · Nitrate ion · ion · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 200 | 0.64 | 0.84 | 39 | empty |
| 2 | 567 | 0.62 | 0.74 | 60 | empty |
| 3 | 225 | 0.57 | 0.79 | 33 | empty |
| 4 | 72 | 0.52 | 0.85 | 19 | empty |
| 5 | 164 | 0.51 | 0.78 | 21 | empty |
Interfaces
8 interfaces between chains.
- H–L · 1822 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 846 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 827 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 592 Ų buried · 9 hydrogen bonds · protein-protein
- B–H · 382 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 6OEL · Engineered Fab bound to IL-4 receptor · the same entry in another collection · chain L against L, 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 B against A, TM-score 0.99
- P31785 · AlphaFold monomer V2.0 prediction for cytokine receptor common subunit gamma (P31785) · a predicted model of the same protein · chain C against A, TM-score 0.97
- P05112 · AlphaFold monomer V2.0 prediction for interleukin-4 (P05112) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P05112
- Every structure of UniProt P24394
- Every structure of UniProt P31785
- Elsewhere: RCSB PDB 6OEL · PDBe 6OEL · UniProt P05112 · UniProt P24394 · UniProt P31785
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