MolNFT v1 · #189724 · protein
Crystal structure of a Fab-like fragment of anti-mesothelin antibody
7VSW · Light chain: “Crystal structure of a Fab-like fragment of anti-mesothelin antibody”. X-ray diffraction, 18 pockets (best druggability 0.65). MolNFT v1 #189724 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7VSW
- Type
- protein
- Length
- 1,739 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain; Heavy chain
- Pockets
- 18 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I, M | Light chain | protein | 211 | 8% helix, 51% strand | — |
| B | Heavy chain | protein | 226 | 10% helix, 50% strand | — |
| F, J, N | Heavy chain | protein | 223 | 9% helix, 50% strand | — |
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 751 | 0.65 | 0.74 | 68 | empty |
| 2 | 711 | 0.65 | 0.74 | 59 | empty |
| 3 | 709 | 0.64 | 0.74 | 67 | empty |
| 4 | 650 | 0.63 | 0.74 | 61 | empty |
| 5 | 323 | 0.62 | 0.79 | 41 | empty |
Interfaces
9 interfaces between chains.
- E–F · 1919 Ų buried · 12 hydrogen bonds · protein-protein
- M–N · 1918 Ų buried · 12 hydrogen bonds · protein-protein
- I–J · 1909 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1900 Ų buried · 14 hydrogen bonds · protein-protein
- F–J · 1104 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 7VSW · Crystal structure of a Fab-like fragment of anti-mesothelin antibody · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 7VSW · PDBe 7VSW
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