MolNFT v1 · #113713 · protein
Crystal structure of IgE Fc in complex with a neutralizing antibody
5ANM · Immunoglobulin G: “Crystal structure of IgE Fc in complex with a neutralizing antibody”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.69). MolNFT v1 #113713 on GenesisL1: 3D structure, binding sites…
- PDB
- 5ANM
- Type
- protein
- Length
- 1,887 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin G; Ig epsilon chain C region
- UniProt
- P01854
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 8 distinct chains · 7% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Immunoglobulin G | protein | 213 | 8% helix, 45% strand | — |
| B | Immunoglobulin G | protein | 220 | 10% helix, 48% strand | — |
| D | Immunoglobulin G | protein | 219 | 10% helix, 49% strand | — |
| E | Ig epsilon chain C region | protein | 206 | 7% helix, 44% strand | P01854 |
| F | Ig epsilon chain C region | protein | 208 | 9% helix, 47% strand | P01854 |
| G | Ig epsilon chain C region | protein | 211 | 10% helix, 46% strand | P01854 |
| H | Immunoglobulin G | protein | 208 | 1% helix, 49% strand | — |
| L | Immunoglobulin G | protein | 189 | 0% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains D, E, F, H, G
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains E, D, H
- BMA · beta-D-mannopyranose · sugar · 5 copies · chains E, F, D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 275 | 0.69 | 0.84 | 52 | empty |
| 2 | 221 | 0.57 | 0.79 | 26 | empty |
| 3 | 202 | 0.57 | 0.80 | 30 | empty |
| 4 | 182 | 0.56 | 0.80 | 24 | empty |
| 5 | 225 | 0.55 | 0.78 | 23 | empty |
Interfaces
17 interfaces between chains.
- C–D · 1580 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1572 Ų buried · 15 hydrogen bonds · protein-protein
- H–L · 1431 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 1169 Ų buried · 12 hydrogen bonds · protein-protein
- E–H · 678 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5ANM · Crystal structure of IgE Fc in complex with a neutralizing antibody · the same entry in another collection · chain L against L, TM-score 1.00
- P01854 · AlphaFold monomer V2.0 prediction for immunoglobulin heavy constant epsilon (P01854) · a predicted model of the same protein · chain F against A, TM-score 0.93
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 5ANM · PDBe 5ANM · UniProt P01854
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