MolNFT v1 · #59160 · protein
Crystal structure of the IL13-IL4R-IL13RA ternary complex
3BPO · Interleukin 13: “Crystal structure of the IL13-IL4R-IL13RA ternary complex”. X-ray diffraction, 1 ligand (NAG), 8 pockets (best druggability 0.61). MolNFT v1 #59160 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3BPO
- Type
- protein
- Length
- 582 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin 13; Interleukin-4 receptor alpha chain; Interleukin-13 receptor alpha-1 chain
- UniProt
- Q4VB50, P24394, P78552
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin 13 | protein | 98 | 51% helix, 4% strand | Q4VB50 |
| B | Interleukin-4 receptor alpha chain | protein | 198 | 5% helix, 48% strand | P24394 |
| C | Interleukin-13 receptor alpha-1 chain | protein | 286 | 1% helix, 47% strand | P78552 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 122 | 0.61 | 0.86 | 27 | empty |
| 2 | 292 | 0.57 | 0.77 | 41 | empty |
| 3 | 225 | 0.55 | 0.78 | 31 | empty |
| 4 | 162 | 0.49 | 0.77 | 17 | empty |
| 5 | 133 | 0.47 | 0.78 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–C · 838 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 693 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 643 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 11 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3BPO · Crystal structure of the IL13-IL4R-IL13Ra ternary complex · 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 0.98
- 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 0.96
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 Q4VB50
- Every structure of UniProt P24394
- Every structure of UniProt P78552
- Elsewhere: RCSB PDB 3BPO · PDBe 3BPO · UniProt Q4VB50 · UniProt P24394 · UniProt P78552
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