MolNFT v1 · #36624 · protein
Refined crystal structure of the galactan-binding immunoglobulin Fab J539 at 1.95-ångströms resolution
2FBJ · IgA-kappa J539 Fab (light chain): “Refined crystal structure of the galactan-binding immunoglobulin Fab J539 at 1.95-ångströms resolution”. X-ray diffraction, 3 ligands (NAG, FUC, ZN), 5 pockets (best druggability 0.65). MolNFT v1…
- PDB
- 2FBJ
- Type
- protein
- Length
- 433 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IgA-kappa J539 Fab (light chain); IgA-kappa J539 Fab (heavy chain)
- UniProt
- P01810
- Ligands
- NAG, FUC, ZN
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | IgA-kappa J539 Fab (light chain) | protein | 213 | 6% helix, 54% strand | — |
| H | IgA-kappa J539 Fab (heavy chain) | protein | 220 | 4% helix, 51% strand | P01810 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains L, H
- FUC · alpha-L-fucopyranose · sugar
- ZN · Zinc ion · metal
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 | 655 | 0.65 | 0.75 | 67 | empty |
| 2 | 58 | 0.33 | 0.76 | 12 | ZN |
| 3 | 61 | 0.29 | 0.74 | 18 | empty |
| 4 | 56 | 0.28 | 0.75 | 18 | empty |
| 5 | 61 | 0.28 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- L–H · 1877 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2FBJ · Refined crystal structure of the galactan-binding immunoglobulin Fab J539 at… · the same entry in another collection · chain H against H, TM-score 1.00
- P01810 · AlphaFold monomer V2.0 prediction for ig heavy chain V region J539 (P01810) · a predicted model of the same protein · chain H against A, TM-score 0.53
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 P01810
- Elsewhere: RCSB PDB 2FBJ · PDBe 2FBJ · UniProt P01810
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