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The crystal structure of an Fab fragment that binds to the melanoma-associated GD2 ganglioside
Analyse The crystal structure of an Fab fragment that binds to the melanoma-associated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PSK
- Type
- protein
- Length
- 411 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody
- UniProt
- P01837
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Antibody | protein | 213 | 5% helix, 50% strand | P01837 |
| H | Antibody | protein | 198 | 5% helix, 53% strand | — |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.51 | 0.74 | 47 | empty |
| 2 | 52 | 0.44 | 0.83 | 17 | empty |
| 3 | 79 | 0.33 | 0.75 | 18 | empty |
| 4 | 62 | 0.30 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- L–H · 1711 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1PSK · The crystal structure of an Fab fragment that binds to the melanoma-associated GD2… · the same entry in another collection · chain L against L, TM-score 1.00
- P01837 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa constant (P01837) · a predicted model of the same protein · chain L against A, TM-score 0.49
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 P01837
- Elsewhere: RCSB PDB 1PSK · PDBe 1PSK · UniProt P01837
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