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Crystal structure of the IgE-FC3-4 domains
Analyse Crystal structure of the IgE-FC3-4 domains in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H9Y
- Type
- protein
- Length
- 628 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ig epsilon chain C region
- UniProt
- P01854
- Ligands
- MAN, NAG, BMA, NH4
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Ig epsilon chain C region | protein | 209 | 11% helix, 46% strand | P01854 |
| B | Ig epsilon chain C region | protein | 210 | 10% helix, 47% strand | P01854 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 7 copies · chains A, B, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, E
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A, B, E
- NH4 · Ammonium ion · ion · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 747 | 0.68 | 0.76 | 72 | empty |
| 2 | 247 | 0.51 | 0.75 | 35 | empty |
| 3 | 292 | 0.51 | 0.74 | 38 | empty |
| 4 | 186 | 0.46 | 0.75 | 25 | empty |
| 5 | 160 | 0.41 | 0.73 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 553 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 161 Ų buried · 0 hydrogen bonds · protein-protein
- B–E · 101 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
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 P01854
- Elsewhere: RCSB PDB 3H9Y · PDBe 3H9Y · UniProt P01854
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