Research workbench
Novel Anti-Mesothelin Antibodies Enable Crystallography of the Intact Mesothelin Ectodo- main and Engineering of Potent, T cell-engaging Bispecific Therapeutics
Analyse Novel Anti-Mesothelin Antibodies Enable Crystallography of the Intact… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8CXC
- Type
- protein
- Length
- 938 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.31
- Source
- Homo sapiens; Mus musculus
- Molecule
- 3F2 Antibody light chain; 3F2 Antibody heavy chain; Mesothelin, cleaved form; scFv…
- UniProt
- Q13421
- Pockets
- 14 · best druggability 0.69
Structure
x-ray diffraction · resolution 4.31 · 4 distinct chains · 17% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | 3F2 Antibody light chain | protein | 212 | 7% helix, 48% strand | — |
| H | 3F2 Antibody heavy chain | protein | 217 | 1% helix, 49% strand | — |
| M | Mesothelin, cleaved form | protein | 288 | 51% helix, 0% strand | Q13421 |
| A | scFv Amatuximab | protein | 221 | 0% helix, 44% strand | — |
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.69 | 0.96 | 16 | empty |
| 2 | 131 | 0.64 | 0.87 | 30 | empty |
| 3 | 219 | 0.63 | 0.82 | 33 | empty |
| 4 | 419 | 0.60 | 0.75 | 44 | empty |
| 5 | 73 | 0.60 | 0.89 | 22 | empty |
Interfaces
4 interfaces between chains.
- L–H · 1870 Ų buried · 10 hydrogen bonds · protein-protein
- M–A · 858 Ų buried · 4 hydrogen bonds · protein-protein
- H–M · 351 Ų buried · 3 hydrogen bonds · protein-protein
- L–M · 265 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- Q13421 · AlphaFold monomer V2.0 prediction for mesothelin (Q13421) · a predicted model of the same protein · chain M against A, TM-score 0.60
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 Q13421
- Elsewhere: RCSB PDB 8CXC · PDBe 8CXC · UniProt Q13421
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