Research workbench
An engineered disulfide bond reversibly traps the IgE-FC3-4 in a closed, non-receptor binding conformation
Analyse An engineered disulfide bond reversibly traps the IgE-FC3-4 in a closed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GT7
- Type
- protein
- Length
- 852 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ig epsilon chain C region
- UniProt
- P01854
- Ligands
- NAG, MAN, BMA
- Pockets
- 11 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ig epsilon chain C region | protein | 212 | 9% helix, 48% strand | P01854 |
| B, D | Ig epsilon chain C region | protein | 213 | 9% helix, 47% strand | P01854 |
| C | Ig epsilon chain C region | protein | 214 | 9% helix, 47% strand | P01854 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 7 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 325 | 0.51 | 0.73 | 38 | empty |
| 2 | 54 | 0.39 | 0.81 | 21 | empty |
| 3 | 154 | 0.39 | 0.73 | 21 | empty |
| 4 | 92 | 0.38 | 0.76 | 10 | empty |
| 5 | 52 | 0.38 | 0.81 | 19 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1569 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1449 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 185 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 184 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 10 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4GT7 · An engineered disulfide bond reversibly traps the IgE-Fc3-4 in a closed, non-receptor… · the same entry in another collection · chain A against A, TM-score 1.00
- P01854 · AlphaFold monomer V2.0 prediction for immunoglobulin heavy constant epsilon (P01854) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 4GT7 · PDBe 4GT7 · UniProt P01854
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