MolNFT v1 · #117309 · protein
Engineered interleukin-13 bound to receptor
5E4E: “Engineered interleukin-13 bound to receptor”. X-ray diffraction, 2 ligands (NAG, SO4), 8 pockets (best druggability 0.63). MolNFT v1 #117309 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5E4E
- Type
- protein
- Length
- 597 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-13; Interleukin-4 receptor subunit alpha; Interleukin-13 receptor subunit…
- UniProt
- P35225, P24394, P78552
- Ligands
- NAG, SO4
- Pockets
- 8 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-13 | protein | 111 | 50% helix, 5% strand | P35225 |
| B | Interleukin-4 receptor subunit alpha | protein | 183 | 2% helix, 46% strand | P24394 |
| C | Interleukin-13 receptor subunit alpha-1 | protein | 303 | 2% helix, 48% strand | P78552 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, C
- SO4 · Sulfate ion · ion · 7 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 268 | 0.63 | 0.81 | 38 | empty |
| 2 | 559 | 0.62 | 0.74 | 49 | SO4 |
| 3 | 141 | 0.60 | 0.84 | 26 | empty |
| 4 | 183 | 0.54 | 0.79 | 35 | empty |
| 5 | 153 | 0.45 | 0.75 | 32 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1025 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 720 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 657 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5E4E · Engineered Interleukin-13 bound to receptor · the same entry in another collection · chain A against A, TM-score 1.00
- P78552 · AlphaFold monomer V2.0 prediction for interleukin-13 receptor subunit alpha-1 (P78552) · a predicted model of the same protein · chain C against A, TM-score 0.99
- 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 0.97
- P35225 · AlphaFold monomer V2.0 prediction for interleukin-13 (P35225) · a predicted model of the same protein · chain A against A, TM-score 0.89
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 P35225
- Every structure of UniProt P24394
- Every structure of UniProt P78552
- Elsewhere: RCSB PDB 5E4E · PDBe 5E4E · UniProt P35225 · UniProt P24394 · UniProt P78552
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