Research workbench
Crystal structure of il-23 in complex with neutralizing Fab
Analyse Crystal structure of il-23 in complex with neutralizing Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D85
- Type
- protein
- Length
- 852 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab of antibody 7G10, light chain; Fab of antibody 7G10, heavy chain; Interleukin-23…
- UniProt
- Q9NPF7, P29460
- Pockets
- 9 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab of antibody 7G10, light chain | protein | 213 | 7% helix, 51% strand | — |
| B | Fab of antibody 7G10, heavy chain | protein | 216 | 10% helix, 50% strand | — |
| C | Interleukin-23 subunit P19 | protein | 133 | 71% helix, 0% strand | Q9NPF7 |
| D | Interleukin-12 subunit P40 | protein | 290 | 2% helix, 54% strand | P29460 |
Ligands and binding sites
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B, C
- IMD · Imidazole · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 762 | 0.67 | 0.75 | 60 | empty |
| 2 | 128 | 0.61 | 0.86 | 28 | empty |
| 3 | 50 | 0.55 | 0.90 | 18 | empty |
| 4 | 229 | 0.54 | 0.77 | 33 | empty |
| 5 | 142 | 0.52 | 0.80 | 23 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1731 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 933 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 496 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 362 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 3D85 · Crystal structure of IL-23 in complex with neutralizing FAB · 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 0.95
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 3D85 · PDBe 3D85 · UniProt Q9NPF7 · UniProt P29460
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