Research workbench
IgE-Fc in complex with darpins E2_79 and E3_53
Analyse IgE-Fc in complex with darpins E2_79 and E3_53 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MXI
- Type
- protein
- Length
- 970 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IgE Fc; Darpin E3_53; Anti-IgE inhibitor E2_79
- UniProt
- P01854, L7MTK7
- Ligands
- NAG, BMA, FUC
- Pockets
- 12 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | IgE Fc | protein | 211 | 9% helix, 46% strand | P01854 |
| C, D | Darpin E3_53 | protein | 154 | 55% helix, 0% strand | — |
| E, F | Anti-IgE inhibitor E2_79 | protein | 120 | 55% helix, 0% strand | L7MTK7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 327 | 0.59 | 0.77 | 38 | empty |
| 2 | 202 | 0.55 | 0.79 | 26 | empty |
| 3 | 236 | 0.51 | 0.76 | 28 | empty |
| 4 | 102 | 0.41 | 0.77 | 23 | empty |
| 5 | 87 | 0.38 | 0.76 | 18 | empty |
Interfaces
7 interfaces between chains.
- A–C · 1095 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1060 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 1022 Ų buried · 19 hydrogen bonds · protein-protein
- B–E · 806 Ų buried · 11 hydrogen bonds · protein-protein
- A–F · 737 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7MXI · IgE-Fc in complex with DARPins E2_79 and E3_53 · 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
- Every structure of UniProt P01854
- Every structure of UniProt L7MTK7
- Elsewhere: RCSB PDB 7MXI · PDBe 7MXI · UniProt P01854 · UniProt L7MTK7
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