MolNFT v1 · #60987 · protein
Crystal structure of interleukin-23
3D87 · Interleukin-23 subunit P19: “Crystal structure of interleukin-23”. X-ray diffraction, 3 ligands (MAN, K, PO4), 8 pockets (best druggability 0.75). MolNFT v1 #60987 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3D87
- Type
- protein
- Length
- 914 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-23 subunit P19; Interleukin-12 subunit P40
- UniProt
- Q9NPF7, P29460
- Ligands
- MAN, K, PO4
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-23 subunit P19 | protein | 161 | 56% helix, 1% strand | Q9NPF7 |
| B | Interleukin-12 subunit P40 | protein | 298 | 2% helix, 50% strand | P29460 |
| C | Interleukin-23 subunit P19 | protein | 159 | 60% helix, 0% strand | Q9NPF7 |
| D | Interleukin-12 subunit P40 | protein | 296 | 2% helix, 41% strand | P29460 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · chains D
- K · Potassium ion · metal · 2 copies · chains B, D
- PO4 · Phosphate ion · ion · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 995 | 0.75 | 0.78 | 66 | empty |
| 2 | 532 | 0.61 | 0.74 | 50 | empty |
| 3 | 225 | 0.57 | 0.79 | 34 | empty |
| 4 | 107 | 0.56 | 0.85 | 27 | empty |
| 5 | 149 | 0.55 | 0.81 | 27 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1038 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 972 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 827 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 83 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 27 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3D87 · Crystal 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 D against A, TM-score 0.96
- 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 0.91
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 3D87 · PDBe 3D87 · UniProt Q9NPF7 · UniProt P29460
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