Research workbench
Molecular basis of cross-reactivity and the limits of antibody-antigen complementarity
Analyse Molecular basis of cross-reactivity and the limits of antibody-antigen… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DBK
- Type
- protein
- Length
- 435 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG1-kappa DB3 Fab (light chain); IGG1-kappa DB3 Fab (heavy chain)
- UniProt
- P01868
- Ligands
- ANO
- Pockets
- 6 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | IGG1-kappa DB3 Fab (light chain) | protein | 216 | 6% helix, 48% strand | — |
| H | IGG1-kappa DB3 Fab (heavy chain) | protein | 219 | 7% helix, 53% strand | P01868 |
Ligands and binding sites
- ANO · 5-beta-androstane-3,17-dione · ligand · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 161 | 0.53 | 0.79 | 20 | ANO |
| 2 | 156 | 0.42 | 0.74 | 32 | empty |
| 3 | 120 | 0.42 | 0.76 | 21 | empty |
| 4 | 52 | 0.37 | 0.80 | 17 | empty |
| 5 | 86 | 0.35 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- L–H · 1773 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1DBK · Molecular basis of cross-reactivity and the limits of antibody-antigen complementarity · the same entry in another collection · chain L against L, TM-score 1.00
- P01868 · AlphaFold monomer V2.0 prediction for ig gamma-1 chain C region secreted form (P01868) · 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 P01868
- Elsewhere: RCSB PDB 1DBK · PDBe 1DBK · UniProt P01868
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.