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Crystal structure of ectodomain 3 of the IL-13 receptor alpha 1 in complex with a human neutralizing monoclonal antibody fragment
Analyse Crystal structure of ectodomain 3 of the IL-13 receptor alpha 1 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HWB
- Type
- protein
- Length
- 539 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.61
- Source
- Homo sapiens
- Molecule
- Interleukin-13 receptor subunit alpha-1; Fab heavy chain; Fab light chain
- UniProt
- P78552
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.56
Structure
x-ray diffraction · resolution 2.61 · 3 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-13 receptor subunit alpha-1 | protein | 111 | 6% helix, 36% strand | P78552 |
| H | Fab heavy chain | protein | 216 | 7% helix, 51% strand | — |
| L | Fab light chain | protein | 212 | 7% helix, 53% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 13 copies · chains A, L, H
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 5 copies · chains A, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 384 | 0.56 | 0.74 | 55 | empty |
| 2 | 324 | 0.55 | 0.75 | 38 | SO4 |
| 3 | 270 | 0.52 | 0.75 | 34 | NHE |
| 4 | 65 | 0.49 | 0.85 | 22 | empty |
| 5 | 126 | 0.41 | 0.75 | 24 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1663 Ų buried · 11 hydrogen bonds · protein-protein
- A–H · 832 Ų buried · 21 hydrogen bonds · protein-protein
- A–L · 412 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4HWB · Crystal structure of ectodomain 3 of the il-13 receptor alpha 1 in complex with a human… · 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 A against A, TM-score 0.46
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 P78552
- Elsewhere: RCSB PDB 4HWB · PDBe 4HWB · UniProt P78552
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