Research workbench
Il-23:IL-23R:NB22E11 complex
Analyse Il-23:IL-23R:NB22E11 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MZV
- Type
- protein
- Length
- 856 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-12 subunit beta; Interleukin-23 subunit alpha; Interleukin-23 receptor…
- UniProt
- P29460, Q9NPF7, Q5VWK5
- Ligands
- NAG, MAN, BMA, NA, CL
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-12 subunit beta | protein | 303 | 2% helix, 52% strand | P29460 |
| B | Interleukin-23 subunit alpha | protein | 137 | 67% helix, 1% strand | Q9NPF7 |
| C | Interleukin-23 receptor | protein | 293 | 1% helix, 52% strand | Q5VWK5 |
| D | Nanobody 22E11 | protein | 123 | 5% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, C
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · 3 copies · chains A, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 792 | 0.73 | 0.78 | 74 | NAG |
| 2 | 115 | 0.52 | 0.82 | 19 | empty |
| 3 | 91 | 0.42 | 0.79 | 20 | empty |
| 4 | 114 | 0.41 | 0.76 | 25 | empty |
| 5 | 72 | 0.33 | 0.75 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–B · 983 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 936 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 885 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 272 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 5MZV · IL-23:IL-23R:Nb22E11 complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q5VWK5 · AlphaFold monomer V2.0 prediction for interleukin-23 receptor (Q5VWK5) · a predicted model of the same protein · chain C 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 B against A, TM-score 0.95
- 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 0.95
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 P29460
- Every structure of UniProt Q9NPF7
- Every structure of UniProt Q5VWK5
- Elsewhere: RCSB PDB 5MZV · PDBe 5MZV · UniProt P29460 · UniProt Q9NPF7 · UniProt Q5VWK5
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