Research workbench
Crystal structure of IL23 bound to peptide 23-652
Analyse Crystal structure of IL23 bound to peptide 23-652 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UIB
- Type
- protein
- Length
- 421 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-23 subunit alpha; Interleukin-12 subunit beta; Peptide 23-652
- UniProt
- Q9NPF7, P29460
- Ligands
- NAG
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-23 subunit alpha | protein | 132 | 70% helix, 0% strand | Q9NPF7 |
| B | Interleukin-12 subunit beta | protein | 274 | 3% helix, 50% strand | P29460 |
| C | Peptide 23-652 | protein | 15 | 67% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.56 | 0.83 | 32 | empty |
| 2 | 293 | 0.54 | 0.75 | 41 | empty |
| 3 | 68 | 0.31 | 0.74 | 15 | empty |
| 4 | 53 | 0.29 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1020 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 457 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 392 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6UIB · Crystal structure of IL23 bound to peptide 23-652 · 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 B against A, TM-score 0.99
- Q9NPF7 · AlphaFold monomer V2.0 prediction for interleukin-23 subunit alpha (Q9NPF7) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 6UIB · PDBe 6UIB · UniProt Q9NPF7 · UniProt P29460
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