Research workbench
Crystal structure of ustekinumab FAB/IL-12 complex
Analyse Crystal structure of ustekinumab FAB/IL-12 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HMX
- Type
- protein
- Length
- 902 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-12 subunit beta; Interleukin-12 subunit alpha; Ustekinumab Fab light chain…
- UniProt
- P29460, P29459
- Ligands
- NAG, MAN, BMA
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-12 subunit beta | protein | 295 | 2% helix, 41% strand | P29460 |
| B | Interleukin-12 subunit alpha | protein | 176 | 54% helix, 0% strand | P29459 |
| L | Ustekinumab Fab light chain | protein | 214 | 6% helix, 48% strand | — |
| H | Ustekinumab Fab heavy chain | protein | 217 | 6% helix, 52% 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 666 | 0.72 | 0.79 | 75 | empty |
| 2 | 469 | 0.60 | 0.75 | 45 | empty |
| 3 | 66 | 0.56 | 0.88 | 24 | empty |
| 4 | 54 | 0.54 | 0.89 | 19 | empty |
| 5 | 191 | 0.50 | 0.77 | 32 | empty |
Interfaces
4 interfaces between chains.
- L–H · 1878 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1012 Ų buried · 12 hydrogen bonds · protein-protein
- A–H · 677 Ų buried · 14 hydrogen bonds · protein-protein
- A–L · 393 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3HMX · Crystal structure of ustekinumab FAB/IL-12 complex · 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 0.95
- P29459 · AlphaFold monomer V2.0 prediction for interleukin-12 subunit alpha (P29459) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 P29459
- Elsewhere: RCSB PDB 3HMX · PDBe 3HMX · UniProt P29460 · UniProt P29459
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