Research workbench
The complex of human IgE-Fc with two bound Fab fragments
Analyse The complex of human IgE-Fc with two bound Fab fragments in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J4P
- Type
- protein
- Length
- 1,508 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ig epsilon chain C region; Immunoglobulin G Fab fragment heavy chain; Immunoglobulin G…
- UniProt
- P01854
- Ligands
- BMA, NAG
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 5% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ig epsilon chain C region | protein | 315 | 5% helix, 50% strand | P01854 |
| B | Ig epsilon chain C region | protein | 317 | 8% helix, 46% strand | P01854 |
| H | Immunoglobulin G Fab fragment heavy chain | protein | 224 | 4% helix, 49% strand | — |
| L, D | Immunoglobulin G Fab fragment light chain | protein | 215 | 5% helix, 51% strand | — |
| C | Immunoglobulin G Fab fragment heavy chain | protein | 222 | 1% helix, 51% strand | — |
Ligands and binding sites
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains A, C, B, H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, H, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1020 | 0.83 | 0.84 | 110 | empty |
| 2 | 329 | 0.61 | 0.78 | 49 | empty |
| 3 | 555 | 0.60 | 0.74 | 64 | empty |
| 4 | 74 | 0.55 | 0.87 | 16 | NAG |
| 5 | 356 | 0.52 | 0.73 | 46 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2438 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 1838 Ų buried · 9 hydrogen bonds · protein-protein
- H–L · 1800 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 747 Ų buried · 7 hydrogen bonds · protein-protein
- A–H · 712 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4J4P · The complex of human IgE-Fc with two bound Fab fragments · the same entry in another collection · chain D against D, TM-score 1.00
- P01854 · AlphaFold monomer V2.0 prediction for immunoglobulin heavy constant epsilon (P01854) · a predicted model of the same protein · chain B against A, TM-score 0.66
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 4J4P · PDBe 4J4P · UniProt P01854
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