MolNFT v1 · #127168 · protein
Crystal structure of human IgE-Fc epsilon 3-4
5MOI · Ig epsilon chain C region: “Crystal structure of human IgE-Fc epsilon 3-4”. X-ray diffraction, 4 ligands (MAN, NAG, BMA), 11 pockets (best druggability 0.81). MolNFT v1 #127168 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5MOI
- Type
- protein
- Length
- 1,145 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ig epsilon chain C region
- UniProt
- P01854
- Ligands
- MAN, NAG, BMA, PO4
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ig epsilon chain C region | protein | 177 | 12% helix, 45% strand | P01854 |
| B | Ig epsilon chain C region | protein | 191 | 10% helix, 47% strand | P01854 |
| C | Ig epsilon chain C region | protein | 208 | 9% helix, 48% strand | P01854 |
| D | Ig epsilon chain C region | protein | 193 | 10% helix, 48% strand | P01854 |
| E | Ig epsilon chain C region | protein | 200 | 11% helix, 48% strand | P01854 |
| F | Ig epsilon chain C region | protein | 176 | 12% helix, 44% strand | P01854 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 14 copies · chains A, B, C, D, E, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B, C, D, E
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 6 copies · chains B, C, D, E, F
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B, D
- EDO · 1,2-ethanediol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 830 | 0.81 | 0.84 | 101 | PEG |
| 2 | 350 | 0.71 | 0.83 | 61 | empty |
| 3 | 187 | 0.44 | 0.74 | 28 | empty |
| 4 | 201 | 0.44 | 0.73 | 23 | MAN, PEG |
| 5 | 105 | 0.42 | 0.78 | 21 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1076 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1053 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 983 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 559 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 469 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
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 5MOI · PDBe 5MOI · UniProt P01854
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