Research workbench
Interleukin-23 complex with an antagonistic alphabody, crystal form 1
Analyse Interleukin-23 complex with an antagonistic alphabody, crystal form 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MJ3
- Type
- protein
- Length
- 544 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-12 subunit beta; Interleukin-23 subunit alpha; Alphabody MA12
- UniProt
- P29460, Q9NPF7
- Ligands
- NAG, MAN, BMA, NA
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-12 subunit beta | protein | 302 | 2% helix, 53% strand | P29460 |
| B | Interleukin-23 subunit alpha | protein | 155 | 65% helix, 0% strand | Q9NPF7 |
| C | Alphabody MA12 | protein | 87 | 83% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- PGE · Triethylene glycol · additive · 2 copies · chains A
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 829 | 0.74 | 0.78 | 88 | empty |
| 2 | 116 | 0.62 | 0.87 | 27 | empty |
| 3 | 58 | 0.26 | 0.73 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1303 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 848 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 42 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, alkylation).
Compared structures
- 5MJ3 · Interleukin-23 complex with an antagonistic alphabody, crystal form 1 · 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 A 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 0.94
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
- Elsewhere: RCSB PDB 5MJ3 · PDBe 5MJ3 · UniProt P29460 · UniProt Q9NPF7
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