MolNFT v1 · #122825 · protein
Structural basis for tslp antagonism by the therapeutic antibody tezepelumab (MEDI9929 / amg-157)
5J13 · Thymic stromal lymphopoietin: “Structural basis for tslp antagonism by the therapeutic antibody tezepelumab (MEDI9929 / amg-157)”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.65). MolNFT v1 #122825 on…
- PDB
- 5J13
- Type
- protein
- Length
- 531 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymic stromal lymphopoietin; Anti-tslp Fab-fragment, light chain; Anti-tslp…
- UniProt
- Q969D9
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymic stromal lymphopoietin | protein | 109 | 60% helix, 2% strand | Q969D9 |
| B | Anti-tslp Fab-fragment, light chain | protein | 213 | 8% helix, 50% strand | — |
| C | Anti-tslp Fab-fragment, heavy chain | protein | 209 | 4% helix, 54% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 614 | 0.65 | 0.75 | 59 | empty |
| 2 | 298 | 0.61 | 0.79 | 39 | empty |
| 3 | 89 | 0.41 | 0.78 | 24 | empty |
| 4 | 69 | 0.33 | 0.76 | 13 | empty |
| 5 | 96 | 0.32 | 0.73 | 25 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1808 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 636 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 34 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5J13 · Structural basis for TSLP antagonism by the therapeutic antibody Tezepelumab (MEDI9929 /… · the same entry in another collection · chain A against A, TM-score 1.00
- Q969D9 · AlphaFold monomer V2.0 prediction for thymic stromal lymphopoietin (Q969D9) · a predicted model of the same protein · chain A 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 Q969D9
- Elsewhere: RCSB PDB 5J13 · PDBe 5J13 · UniProt Q969D9
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