Research workbench
Structure of extended IgE-Fc in complex with two anti-IgE fabs
Analyse Structure of extended IgE-Fc in complex with two anti-IgE fabs in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EYO
- Type
- protein
- Length
- 1,439 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin heavy constant epsilon; 8D6 Fab heavy chain; 8D6 Fab light chain
- UniProt
- P01854
- Ligands
- MAN, NAG, BMA
- Pockets
- 17 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 5% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Immunoglobulin heavy constant epsilon | protein | 307 | 9% helix, 48% strand | P01854 |
| B | Immunoglobulin heavy constant epsilon | protein | 309 | 10% helix, 49% strand | P01854 |
| I | 8D6 Fab heavy chain | protein | 208 | 3% helix, 50% strand | — |
| H | 8D6 Fab heavy chain | protein | 204 | 3% helix, 53% strand | — |
| M | 8D6 Fab light chain | protein | 201 | 1% helix, 50% strand | — |
| L | 8D6 Fab light chain | protein | 210 | 2% helix, 50% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 7 copies · chains A, M, L, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, M
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 718 | 0.76 | 0.81 | 85 | empty |
| 2 | 556 | 0.67 | 0.77 | 63 | MAN |
| 3 | 379 | 0.59 | 0.76 | 61 | empty |
| 4 | 376 | 0.55 | 0.74 | 56 | empty |
| 5 | 73 | 0.55 | 0.87 | 17 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2105 Ų buried · 16 hydrogen bonds · protein-protein
- H–L · 1537 Ų buried · 8 hydrogen bonds · protein-protein
- I–M · 1495 Ų buried · 12 hydrogen bonds · protein-protein
- B–I · 824 Ų buried · 10 hydrogen bonds · protein-protein
- A–H · 795 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6EYO · Structure of extended IgE-Fc in complex with two anti-IgE Fabs · the same entry in another collection · chain L against L, 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 0.67
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 6EYO · PDBe 6EYO · UniProt P01854
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