MolNFT v1 · #30437 · protein
Catalytic antibody 5C8, Fab-hapten complex
25C8 · IgG 5C8: “Catalytic antibody 5C8, Fab-hapten complex”. X-ray diffraction, 1 ligand (GEP), 4 pockets (best druggability 0.60). MolNFT v1 #30437 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 25C8
- Type
- protein
- Length
- 429 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IgG 5C8
- UniProt
- P01837, P01869
- Ligands
- GEP
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | IgG 5C8 | protein | 212 | 8% helix, 52% strand | P01837 |
| H | IgG 5C8 | protein | 217 | 4% helix, 51% strand | P01869 |
Ligands and binding sites
- GEP · N-methyl-N-(para-glutaramidophenyl-ethyl)-piperidinium ion · ligand · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 472 | 0.60 | 0.75 | 48 | empty |
| 2 | 208 | 0.58 | 0.80 | 36 | GEP |
| 3 | 140 | 0.42 | 0.75 | 23 | empty |
| 4 | 52 | 0.24 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- L–H · 1673 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 25C8 · Catalytic antibody 5C8, Fab-hapten complex · the same entry in another collection · chain L against L, TM-score 1.00
- P01869 · AlphaFold monomer V2.0 prediction for ig gamma-1 chain C region, membrane-bound form… · a predicted model of the same protein · chain H against A, TM-score 0.49
- P01837 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa constant (P01837) · a predicted model of the same protein · chain L against A, TM-score 0.48
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 P01837
- Every structure of UniProt P01869
- Elsewhere: RCSB PDB 25C8 · PDBe 25C8 · UniProt P01837 · UniProt P01869
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