Research workbench
IgE-Fc in complex with 813
Analyse IgE-Fc in complex with 813 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SI0
- Type
- protein
- Length
- 1,777 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IgE Fc; 813 variable fragment heavy chain; 813 variable fragment light chain
- UniProt
- P01854
- Ligands
- MAN, NAG, BMA, NA
- Pockets
- 16 · best druggability 0.54
Structure
x-ray diffraction · 6 distinct chains · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, G, H, A | IgE Fc | protein | 209 | 8% helix, 46% strand | P01854 |
| I | 813 variable fragment heavy chain | protein | 122 | 5% helix, 56% strand | — |
| J | 813 variable fragment light chain | protein | 112 | 3% helix, 52% strand | — |
| E | 813 variable fragment heavy chain | protein | 123 | 7% helix, 56% strand | — |
| F, D, L | 813 variable fragment light chain | protein | 114 | 3% helix, 51% strand | — |
| C, K | 813 variable fragment heavy chain | protein | 121 | 5% helix, 55% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 9 copies · chains B, G, H, A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains B, G, H, A
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains B, G, H, A
- NA · Sodium ion · metal · 3 copies · chains I, J, E, F, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 308 | 0.54 | 0.75 | 48 | empty |
| 2 | 216 | 0.51 | 0.76 | 30 | empty |
| 3 | 265 | 0.50 | 0.74 | 32 | NA |
| 4 | 204 | 0.50 | 0.77 | 29 | empty |
| 5 | 188 | 0.47 | 0.76 | 31 | empty |
Interfaces
15 interfaces between chains.
- G–H · 1324 Ų buried · 12 hydrogen bonds · protein-protein
- B–A · 1257 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 942 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 932 Ų buried · 9 hydrogen bonds · protein-protein
- K–L · 921 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7SI0 · IgE-Fc in complex with 813 · the same entry in another collection · chain L against L, 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 7SI0 · PDBe 7SI0 · UniProt P01854
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