Research workbench
Structure of a complex of human il-23 with 3 nanobodies (llama vhhs)
Analyse Structure of a complex of human il-23 with 3 nanobodies (llama vhhs) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GRW
- Type
- protein
- Length
- 1,587 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-23 subunit alpha; Interleukin-12 subunit beta; Nanobody 124C4; Nanobody 37D5…
- UniProt
- Q9NPF7, P29460
- Ligands
- NAG, MAN, BMA
- Pockets
- 15 · best druggability 0.74
Structure
x-ray diffraction · 8 distinct chains · 18% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-23 subunit alpha | protein | 130 | 72% helix, 0% strand | Q9NPF7 |
| B | Interleukin-12 subunit beta | protein | 293 | 2% helix, 53% strand | P29460 |
| C | Interleukin-23 subunit alpha | protein | 129 | 74% helix, 0% strand | Q9NPF7 |
| D | Interleukin-12 subunit beta | protein | 292 | 2% helix, 53% strand | P29460 |
| E, G | Nanobody 124C4 | protein | 125 | 7% helix, 50% strand | — |
| F | Nanobody 37D5 | protein | 125 | 8% helix, 41% strand | — |
| H, I | Nanobody 22E11 | protein | 123 | 7% helix, 53% strand | — |
| J | Nanobody 37D5 | protein | 122 | 8% helix, 43% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, D
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains B, D
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 951 | 0.74 | 0.77 | 74 | empty |
| 2 | 680 | 0.72 | 0.79 | 76 | empty |
| 3 | 475 | 0.66 | 0.78 | 57 | empty |
| 4 | 129 | 0.62 | 0.86 | 27 | empty |
| 5 | 525 | 0.61 | 0.75 | 66 | empty |
Interfaces
18 interfaces between chains.
- C–D · 946 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 941 Ų buried · 11 hydrogen bonds · protein-protein
- C–F · 900 Ų buried · 11 hydrogen bonds · protein-protein
- A–J · 873 Ų buried · 11 hydrogen bonds · protein-protein
- D–I · 849 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4GRW · Structure of a complex of human IL-23 with 3 Nanobodies (Llama vHHs) · the same entry in another collection · chain J against J, 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 0.99
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 4GRW · PDBe 4GRW · UniProt Q9NPF7 · UniProt P29460
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