Research workbench
Structure and specificity of the anti-digoxin antibody 40-50
Analyse Structure and specificity of the anti-digoxin antibody 40-50 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IBG
- Type
- protein
- Length
- 434 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG2B-kappa 40-50 Fab (light chain); IGG2B-kappa 40-50 Fab (heavy chain)
- Ligands
- OBN, CU
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | IGG2B-kappa 40-50 Fab (light chain) | protein | 217 | 7% helix, 51% strand | — |
| H | IGG2B-kappa 40-50 Fab (heavy chain) | protein | 217 | 7% helix, 56% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 590 | 0.62 | 0.74 | 55 | empty |
| 2 | 125 | 0.51 | 0.80 | 20 | OBN |
| 3 | 69 | 0.38 | 0.78 | 17 | empty |
| 4 | 58 | 0.33 | 0.77 | 15 | empty |
| 5 | 51 | 0.28 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- L–H · 1936 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1IBG · Structure and specificity of the anti-digoxin antibody 40-50 · the same entry in another collection · chain L against L, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 1IBG · PDBe 1IBG
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