Research workbench
Structure of interleukin-23
Analyse Structure of interleukin-23 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DUH
- Type
- protein
- Length
- 868 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-12 subunit beta; Interleukin-23 subunit alpha
- UniProt
- P29460, Q9NPF7
- Ligands
- NAG
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-12 subunit beta | protein | 300 | 2% helix, 52% strand | P29460 |
| B | Interleukin-12 subunit beta | protein | 294 | 2% helix, 52% strand | P29460 |
| C | Interleukin-23 subunit alpha | protein | 137 | 64% helix, 0% strand | Q9NPF7 |
| D | Interleukin-23 subunit alpha | protein | 137 | 63% helix, 0% strand | Q9NPF7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 277 | 0.76 | 0.89 | 47 | empty |
| 2 | 1054 | 0.76 | 0.79 | 96 | empty |
| 3 | 267 | 0.76 | 0.89 | 47 | empty |
| 4 | 159 | 0.61 | 0.84 | 31 | empty |
| 5 | 163 | 0.53 | 0.80 | 26 | empty |
Interfaces
5 interfaces between chains.
- B–D · 951 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 944 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 933 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 164 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 158 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3DUH · Structure of Interleukin-23 · the same entry in another collection · chain D against D, 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 0.98
- Q9NPF7 · AlphaFold monomer V2.0 prediction for interleukin-23 subunit alpha (Q9NPF7) · a predicted model of the same protein · chain C against A, TM-score 0.92
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 P29460
- Every structure of UniProt Q9NPF7
- Elsewhere: RCSB PDB 3DUH · PDBe 3DUH · UniProt P29460 · UniProt Q9NPF7
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