MolNFT v1 · #16502 · protein
The crystal structure of IgE Fc reveals an asymmetrically bent conformation
1O0V · Immunoglobulin heavy chain epsilon-1: “The crystal structure of IgE Fc reveals an asymmetrically bent conformation”. X-ray diffraction, 4 ligands (MAN, NAG, BMA), 7 pockets (best druggability 0.73). MolNFT v1 #16502 on GenesisL1: 3D…
- PDB
- 1O0V
- Type
- protein
- Length
- 639 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin heavy chain epsilon-1
- Ligands
- MAN, NAG, BMA, SO4
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Immunoglobulin heavy chain epsilon-1 | protein | 319 | 10% helix, 49% strand | — |
| B | Immunoglobulin heavy chain epsilon-1 | protein | 320 | 9% helix, 46% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 7 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 533 | 0.73 | 0.81 | 67 | GOL |
| 2 | 55 | 0.48 | 0.85 | 17 | empty |
| 3 | 193 | 0.47 | 0.75 | 27 | NAG |
| 4 | 145 | 0.39 | 0.73 | 24 | empty |
| 5 | 109 | 0.34 | 0.73 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 2981 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1O0V · The crystal structure of IgE Fc reveals an asymmetrically bent conformation · the same entry in another collection · chain A against A, 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 1O0V · PDBe 1O0V
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