Research workbench
Structure of unbound interleukin-23
Analyse Structure of unbound interleukin-23 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MXA
- Type
- protein
- Length
- 441 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-23 subunit alpha; Interleukin-12 subunit beta
- UniProt
- Q9NPF7, P29460
- Ligands
- NAG, BMA, MAN
- Pockets
- 5 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Interleukin-23 subunit alpha | protein | 140 | 69% helix, 0% strand | Q9NPF7 |
| A | Interleukin-12 subunit beta | protein | 301 | 1% helix, 56% strand | P29460 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar · chains A
- MAN · alpha-D-mannopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.46 | 0.80 | 18 | empty |
| 2 | 62 | 0.41 | 0.81 | 16 | empty |
| 3 | 52 | 0.38 | 0.81 | 17 | empty |
| 4 | 52 | 0.33 | 0.78 | 15 | empty |
| 5 | 52 | 0.25 | 0.72 | 14 | empty |
Interfaces
1 interface between chains.
- B–A · 952 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5MXA · Structure of unbound Interleukin-23 · the same entry in another collection · chain A against A, TM-score 1.00
- P29460 · AlphaFold monomer V2.0 prediction for interleukin-12 subunit beta (P29460) · a predicted model of the same protein · chain A against A, TM-score 0.97
- Q9NPF7 · AlphaFold monomer V2.0 prediction for interleukin-23 subunit alpha (Q9NPF7) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 Q9NPF7
- Every structure of UniProt P29460
- Elsewhere: RCSB PDB 5MXA · PDBe 5MXA · UniProt Q9NPF7 · UniProt P29460
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