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Crystal structure of the Fab fragment of therapeutic antibody daclizumab in complex with il-2RA (CD25) ectodomain
Analyse Crystal structure of the Fab fragment of therapeutic antibody daclizumab in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NFP
- Type
- protein
- Length
- 1,086 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain of Fab fragment of daclizumab; Light chain of Fab fragment of daclizumab…
- UniProt
- P01589
- Pockets
- 17 · best druggability 0.60
Structure
x-ray diffraction · 5 distinct chains · 4% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heavy chain of Fab fragment of daclizumab | protein | 213 | 6% helix, 50% strand | — |
| B, L | Light chain of Fab fragment of daclizumab | protein | 212 | 5% helix, 52% strand | — |
| H | Heavy chain of Fab fragment of daclizumab | protein | 214 | 6% helix, 50% strand | — |
| I | Interleukin-2 receptor subunit alpha | protein | 124 | 0% helix, 35% strand | P01589 |
| K | Interleukin-2 receptor subunit alpha | protein | 111 | 0% helix, 29% strand | P01589 |
Pockets
17 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.60 | 0.88 | 25 | empty |
| 2 | 273 | 0.58 | 0.78 | 35 | empty |
| 3 | 265 | 0.49 | 0.74 | 44 | empty |
| 4 | 144 | 0.48 | 0.78 | 20 | empty |
| 5 | 70 | 0.44 | 0.81 | 16 | empty |
Interfaces
8 interfaces between chains.
- H–L · 1629 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1613 Ų buried · 8 hydrogen bonds · protein-protein
- H–I · 650 Ų buried · 11 hydrogen bonds · protein-protein
- A–K · 520 Ų buried · 15 hydrogen bonds · protein-protein
- L–I · 511 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide (disulfide).
Compared structures
- 3NFP · Crystal structure of the Fab fragment of therapeutic antibody daclizumab 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 K against A, TM-score 0.90
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 3NFP · PDBe 3NFP · UniProt P01589
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