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
- 2DBL
- 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
- S5H
- Pockets
- 5 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | IGG1-kappa DB3 Fab (light chain) | protein | 216 | 6% helix, 46% strand | — |
| H | IGG1-kappa DB3 Fab (heavy chain) | protein | 219 | 10% helix, 52% strand | P01868 |
Ligands and binding sites
- S5H · 5-alpha-pregnane-3-beta-ol-hemisuccinate · ligand · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.54 | 0.81 | 18 | S5H |
| 2 | 118 | 0.45 | 0.78 | 29 | empty |
| 3 | 130 | 0.40 | 0.74 | 22 | empty |
| 4 | 110 | 0.37 | 0.74 | 25 | empty |
| 5 | 84 | 0.35 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- L–H · 1841 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2DBL · 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 2DBL · PDBe 2DBL · UniProt P01868
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