Research workbench
Crystal structure of a glycosylated Fab from an IgM cryoglobulin with properties of a natural proteolytic antibody
Analyse Crystal structure of a glycosylated Fab from an IgM cryoglobulin with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AGJ
- Type
- protein
- Length
- 441 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yvo Fab, light chain; Yvo Fab, heavy chain
- UniProt
- Q6PJF2, P01871
- Ligands
- NAG
- Pockets
- 4 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Yvo Fab, light chain | protein | 215 | 7% helix, 50% strand | Q6PJF2 |
| H | Yvo Fab, heavy chain | protein | 226 | 6% helix, 42% strand | P01871 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 292 | 0.52 | 0.74 | 40 | empty |
| 2 | 93 | 0.34 | 0.74 | 19 | empty |
| 3 | 80 | 0.33 | 0.74 | 19 | empty |
| 4 | 56 | 0.30 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- L–H · 1972 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 2AGJ · Crystal Structure of a glycosylated Fab from an IgM cryoglobulin with properties of a… · the same entry in another collection · chain L against L, TM-score 1.00
- P01871 · AlphaFold monomer V2.0 prediction for immunoglobulin heavy constant mu (P01871) · a predicted model of the same protein · chain H 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 Q6PJF2
- Every structure of UniProt P01871
- Elsewhere: RCSB PDB 2AGJ · PDBe 2AGJ · UniProt Q6PJF2 · UniProt P01871
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