MolNFT v1 · #168351 · protein
IL23/IL23R/IL12RB1 signaling complex
6WDQ · Interleukin-12 subunit beta: “IL23/IL23R/IL12RB1 signaling complex”. X-ray diffraction, 2 ligands (NAG, BMA), 5 pockets (best druggability 0.83). MolNFT v1 #168351 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6WDQ
- Type
- protein
- Length
- 852 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, P42701
- Ligands
- NAG, BMA
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 43% 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 | 147 | 64% helix, 1% strand | Q9NPF7 |
| C | Interleukin-23 receptor | protein | 293 | 2% helix, 53% strand | Q5VWK5 |
| D | Interleukin-12 receptor subunit beta-1 | protein | 109 | 3% helix, 48% strand | P42701 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, C
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1106 | 0.83 | 0.84 | 98 | empty |
| 2 | 474 | 0.64 | 0.77 | 43 | empty |
| 3 | 87 | 0.49 | 0.83 | 19 | empty |
| 4 | 146 | 0.45 | 0.77 | 30 | empty |
| 5 | 80 | 0.41 | 0.78 | 16 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1104 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1056 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 758 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 332 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 6WDQ · IL23/IL23R/IL12Rb1 signaling complex · 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 A against A, TM-score 0.97
- Q5VWK5 · AlphaFold monomer V2.0 prediction for interleukin-23 receptor (Q5VWK5) · a predicted model of the same protein · chain C against A, TM-score 0.94
- P42701 · AlphaFold monomer V2.0 prediction for interleukin-12 receptor subunit beta-1 (P42701) · a predicted model of the same protein · chain D against A, TM-score 0.93
- 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 0.93
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
- Every structure of UniProt P42701
- Elsewhere: RCSB PDB 6WDQ · PDBe 6WDQ · UniProt P29460 · UniProt Q9NPF7 · UniProt Q5VWK5 · UniProt P42701
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