MolNFT v1 · #4050 · protein
Molecular basis of cross-reactivity and the limits of antibody-antigen complementarity
1DBM · IGG1-kappa DB3 Fab (light chain): “Molecular basis of cross-reactivity and the limits of antibody-antigen complementarity”. X-ray diffraction, 1 ligand (SIH), 6 pockets (best druggability 0.52). MolNFT v1 #4050 on GenesisL1: 3D…
- PDB
- 1DBM
- 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
- SIH
- Pockets
- 6 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | IGG1-kappa DB3 Fab (light chain) | protein | 216 | 6% helix, 47% strand | — |
| H | IGG1-kappa DB3 Fab (heavy chain) | protein | 219 | 8% helix, 51% strand | P01868 |
Ligands and binding sites
- SIH · Progesterone-11-alpha-ol-hemisuccinate · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.52 | 0.82 | 18 | SIH |
| 2 | 178 | 0.51 | 0.78 | 30 | empty |
| 3 | 100 | 0.37 | 0.74 | 23 | empty |
| 4 | 96 | 0.36 | 0.74 | 21 | empty |
| 5 | 60 | 0.33 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- L–H · 1861 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1DBM · 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 1DBM · PDBe 1DBM · UniProt P01868
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