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Crystal structure of a chimeric Fab' fragment of an antibody binding tumour cells
Analyse Crystal structure of a chimeric Fab' fragment of an antibody binding tumour… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BBJ
- Type
- protein
- Length
- 846 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG4-kappa B72.3 Fab (light chain); IGG4-kappa B72.3 Fab (heavy chain)
- UniProt
- P01861
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A | IGG4-kappa B72.3 Fab (light chain) | protein | 211 | 6% helix, 51% strand | — |
| H, B | IGG4-kappa B72.3 Fab (heavy chain) | protein | 212 | 8% helix, 49% strand | P01861 |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 745 | 0.68 | 0.75 | 67 | empty |
| 2 | 705 | 0.67 | 0.75 | 63 | empty |
| 3 | 267 | 0.52 | 0.75 | 38 | empty |
| 4 | 70 | 0.33 | 0.76 | 18 | empty |
| 5 | 63 | 0.29 | 0.74 | 19 | empty |
Interfaces
4 interfaces between chains.
- L–H · 1965 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1961 Ų buried · 16 hydrogen bonds · protein-protein
- L–B · 328 Ų buried · 3 hydrogen bonds · protein-protein
- L–A · 13 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 modified (disulfide, cyclization).
Compared structures
- 1BBJ · Crystal structure of a chimeric Fab' fragment of an antibody binding tumour cells · the same entry in another collection · chain A against A, TM-score 1.00
- P01861 · AlphaFold monomer V2.0 prediction for immunoglobulin heavy constant gamma 4 (P01861) · a predicted model of the same protein · chain H against A, TM-score 0.52
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 P01861
- Elsewhere: RCSB PDB 1BBJ · PDBe 1BBJ · UniProt P01861
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