MolNFT v1 · #119766 · protein
The complex between human IgE-Fc and two anti-IgE Fab fragments
5G64 · Ig epsilon chain C region: “The complex between human IgE-Fc and two anti-IgE Fab fragments”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 17 pockets (best druggability 0.74). MolNFT v1 #119766 on GenesisL1: 3D structure, binding…
- PDB
- 5G64
- Type
- protein
- Length
- 1,463 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ig epsilon chain C region; Fab fragment
- Ligands
- NAG, MAN, BMA
- Pockets
- 17 · best druggability 0.74
Structure
x-ray diffraction · 6 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ig epsilon chain C region | protein | 308 | 9% helix, 50% strand | — |
| B | Ig epsilon chain C region | protein | 306 | 7% helix, 50% strand | — |
| H | Fab fragment | protein | 216 | 6% helix, 54% strand | — |
| I | Fab fragment | protein | 203 | 3% helix, 57% strand | — |
| L | Fab fragment | protein | 216 | 6% helix, 51% strand | — |
| M | Fab fragment | protein | 214 | 4% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
- 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 230 | 0.74 | 0.89 | 41 | empty |
| 2 | 121 | 0.63 | 0.87 | 25 | empty |
| 3 | 424 | 0.57 | 0.74 | 57 | empty |
| 4 | 417 | 0.56 | 0.74 | 43 | empty |
| 5 | 116 | 0.51 | 0.81 | 26 | empty |
Interfaces
8 interfaces between chains.
- A–B · 2007 Ų buried · 25 hydrogen bonds · protein-protein
- H–L · 1793 Ų buried · 14 hydrogen bonds · protein-protein
- I–M · 1645 Ų buried · 11 hydrogen bonds · protein-protein
- B–I · 496 Ų buried · 5 hydrogen bonds · protein-protein
- A–H · 453 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5G64 · The complex between human IgE-Fc and two anti-IgE Fab fragments · 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
- Elsewhere: RCSB PDB 5G64 · PDBe 5G64
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.