Research workbench
IgE-Fc in complex with hae
Analyse IgE-Fc in complex with hae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SHZ
- Type
- protein
- Length
- 1,770 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IgE Fc; Hae variable fragment heavy chain; Hae variable fragment light chain
- UniProt
- P01854
- Ligands
- MAN, NAG, BMA, PO4
- Pockets
- 18 · best druggability 0.68
Structure
x-ray diffraction · 10 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | IgE Fc | protein | 209 | 10% helix, 46% strand | P01854 |
| K | Hae variable fragment heavy chain | protein | 121 | 5% helix, 57% strand | — |
| C | Hae variable fragment heavy chain | protein | 122 | 2% helix, 57% strand | — |
| I | Hae variable fragment heavy chain | protein | 119 | 3% helix, 55% strand | — |
| L, J | Hae variable fragment light chain | protein | 113 | 3% helix, 51% strand | — |
| D, F | Hae variable fragment light chain | protein | 114 | 3% helix, 51% strand | — |
| A | IgE Fc | protein | 210 | 10% helix, 48% strand | P01854 |
| H | IgE Fc | protein | 211 | 12% helix, 46% strand | P01854 |
| G | IgE Fc | protein | 202 | 11% helix, 47% strand | P01854 |
| E | Hae variable fragment heavy chain | protein | 122 | 5% helix, 57% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 10 copies · chains B, A, H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains B, A, H, L, G
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains B, A, H
- PO4 · Phosphate ion · ion · 2 copies · chains C
- EDO · 1,2-ethanediol · additive · 2 copies · chains D, B, E, F
- ACT · Acetate ion · additive · chains C, D
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 734 | 0.68 | 0.76 | 59 | empty |
| 2 | 234 | 0.52 | 0.76 | 39 | empty |
| 3 | 244 | 0.51 | 0.75 | 38 | empty |
| 4 | 184 | 0.50 | 0.77 | 28 | empty |
| 5 | 72 | 0.46 | 0.82 | 17 | ACT |
Interfaces
17 interfaces between chains.
- B–A · 1312 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 954 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 942 Ų buried · 8 hydrogen bonds · protein-protein
- K–L · 933 Ų buried · 9 hydrogen bonds · protein-protein
- I–J · 932 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 5 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 7SHZ · IgE-Fc in complex with HAE · the same entry in another collection · chain F against F, 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
- Elsewhere: RCSB PDB 7SHZ · PDBe 7SHZ · UniProt P01854
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