Research workbench
Major antigen-induced domain rearrangements in an antibody
Analyse Major antigen-induced domain rearrangements in an antibody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GGB
- Type
- protein
- Length
- 430 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG2A-kappa 50.1 Fab (light chain); IGG2A-kappa 50.1 Fab (heavy chain)
- UniProt
- P01865
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | IGG2A-kappa 50.1 Fab (light chain) | protein | 215 | 6% helix, 53% strand | — |
| H | IGG2A-kappa 50.1 Fab (heavy chain) | protein | 215 | 7% helix, 50% strand | P01865 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 342 | 0.53 | 0.74 | 42 | empty |
| 2 | 163 | 0.52 | 0.79 | 20 | empty |
| 3 | 98 | 0.45 | 0.79 | 16 | empty |
| 4 | 65 | 0.28 | 0.72 | 13 | empty |
Interfaces
1 interface between chains.
- L–H · 1704 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1GGB · Major antigen-induced domain rearrangements in an antibody · the same entry in another collection · chain L against L, TM-score 1.00
- P01865 · AlphaFold monomer V2.0 prediction for ig gamma-2A chain C region, membrane-bound form… · a predicted model of the same protein · chain H 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 P01865
- Elsewhere: RCSB PDB 1GGB · PDBe 1GGB · UniProt P01865
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