MolNFT v1 · #67763 · protein
Crystal structure of the Fab fragment of therapeutic antibody basiliximab in complex with il-2RA (CD25) ectodomain
3IU3 · Heavy chain of Fab fragment of basiliximab: “Crystal structure of the Fab fragment of therapeutic antibody basiliximab in complex with il-2RA (CD25)…”. X-ray diffraction, 2 ligands (NAG, BMA), 19 pockets (best druggability 0.71).…
- PDB
- 3IU3
- Type
- protein
- Length
- 1,619 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain of Fab fragment of basiliximab; Light chain of Fab fragment of basiliximab…
- UniProt
- P01589
- Ligands
- NAG, BMA
- Pockets
- 19 · best druggability 0.71
Structure
x-ray diffraction · 6 distinct chains · 4% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, H | Heavy chain of Fab fragment of basiliximab | protein | 215 | 7% helix, 53% strand | — |
| B, L | Light chain of Fab fragment of basiliximab | protein | 208 | 7% helix, 55% strand | — |
| D | Light chain of Fab fragment of basiliximab | protein | 209 | 7% helix, 51% strand | — |
| I | Interleukin-2 receptor alpha chain | protein | 119 | 0% helix, 31% strand | P01589 |
| J | Interleukin-2 receptor alpha chain | protein | 116 | 0% helix, 28% strand | P01589 |
| K | Interleukin-2 receptor alpha chain | protein | 114 | 0% helix, 30% strand | P01589 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains I, J, K
- BMA · beta-D-mannopyranose · sugar · 3 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 853 | 0.71 | 0.77 | 91 | empty |
| 2 | 746 | 0.67 | 0.75 | 77 | empty |
| 3 | 691 | 0.65 | 0.74 | 64 | empty |
| 4 | 560 | 0.60 | 0.73 | 46 | empty |
| 5 | 362 | 0.56 | 0.75 | 51 | empty |
Interfaces
13 interfaces between chains.
- C–D · 1867 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1862 Ų buried · 17 hydrogen bonds · protein-protein
- H–L · 1771 Ų buried · 13 hydrogen bonds · protein-protein
- C–J · 910 Ų buried · 14 hydrogen bonds · protein-protein
- H–I · 889 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 23 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3IU3 · Crystal structure of the Fab fragment of therapeutic antibody Basiliximab in complex with… · the same entry in another collection · chain K against K, TM-score 1.00
- P01589 · AlphaFold monomer V2.0 prediction for interleukin-2 receptor subunit alpha (P01589) · a predicted model of the same protein · chain J against A, TM-score 0.92
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 P01589
- Elsewhere: RCSB PDB 3IU3 · PDBe 3IU3 · UniProt P01589
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