MolNFT v1 · #125691 · protein
Crystal structure of the human IgE-Fc bound to its B cell receptor DERCD23
5LGK · Ig epsilon chain C region: “Crystal structure of the human IgE-Fc bound to its B cell receptor DERCD23”. X-ray diffraction, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.79). MolNFT v1 #125691 on GenesisL1: 3D structure…
- PDB
- 5LGK
- Type
- protein
- Length
- 1,432 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ig epsilon chain C region; Low affinity immunoglobulin epsilon Fc receptor
- UniProt
- P01854, P06734
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ig epsilon chain C region | protein | 307 | 8% helix, 44% strand | P01854 |
| B, D | Ig epsilon chain C region | protein | 304 | 8% helix, 44% strand | P01854 |
| C | Ig epsilon chain C region | protein | 306 | 8% helix, 45% strand | P01854 |
| E | Low affinity immunoglobulin epsilon Fc receptor | protein | 105 | 18% helix, 37% strand | P06734 |
| F | Low affinity immunoglobulin epsilon Fc receptor | protein | 106 | 18% helix, 37% strand | P06734 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B, D, A, C
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains B, D
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 | 1065 | 0.79 | 0.81 | 91 | empty |
| 2 | 812 | 0.77 | 0.81 | 91 | empty |
| 3 | 456 | 0.66 | 0.78 | 60 | empty |
| 4 | 134 | 0.58 | 0.84 | 23 | empty |
| 5 | 264 | 0.57 | 0.78 | 35 | NAG |
Interfaces
7 interfaces between chains.
- C–D · 3016 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2984 Ų buried · 40 hydrogen bonds · protein-protein
- A–E · 1111 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 1037 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 486 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan, 3 disulfide (N-glycosylation, disulfide).
Compared structures
- 5LGK · Crystal structure of the human IgE-Fc bound to its B cell receptor derCD23 · the same entry in another collection · chain F against F, TM-score 1.00
- P06734 · AlphaFold monomer V2.0 prediction for low affinity immunoglobulin epsilon Fc receptor… · a predicted model of the same protein · chain E against A, TM-score 0.95
- P01854 · AlphaFold monomer V2.0 prediction for immunoglobulin heavy constant epsilon (P01854) · a predicted model of the same protein · chain C against A, TM-score 0.74
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
- Every structure of UniProt P06734
- Elsewhere: RCSB PDB 5LGK · PDBe 5LGK · UniProt P01854 · UniProt P06734
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