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Primitive triclinic crystal form of the human IgE-FC(EPSILON)3-4 bound to its B cell receptor DERCD23
Analyse Primitive triclinic crystal form of the human IgE-FC(EPSILON)3-4 bound to its B… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KI1
- Type
- protein
- Length
- 1,366 residues
- Chains
- 8
- 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, MAN, BMA
- Pockets
- 9 · best druggability 0.65
Structure
x-ray diffraction · 6 distinct chains · 13% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Ig epsilon chain C region | protein | 208 | 10% helix, 47% strand | P01854 |
| B, C | Ig epsilon chain C region | protein | 211 | 9% helix, 45% strand | P01854 |
| E | Low affinity immunoglobulin epsilon Fc receptor | protein | 132 | 15% helix, 37% strand | P06734 |
| F | Low affinity immunoglobulin epsilon Fc receptor | protein | 131 | 15% helix, 37% strand | P06734 |
| G | Low affinity immunoglobulin epsilon Fc receptor | protein | 133 | 15% helix, 35% strand | P06734 |
| H | Low affinity immunoglobulin epsilon Fc receptor | protein | 132 | 15% helix, 37% strand | P06734 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 598 | 0.65 | 0.76 | 59 | empty |
| 2 | 104 | 0.47 | 0.80 | 25 | empty |
| 3 | 148 | 0.47 | 0.77 | 25 | empty |
| 4 | 139 | 0.38 | 0.73 | 23 | empty |
| 5 | 139 | 0.38 | 0.73 | 20 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1336 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1315 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 959 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 938 Ų buried · 14 hydrogen bonds · protein-protein
- C–G · 938 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan (N-glycosylation).
Compared structures
- 4KI1 · Primitive triclinic crystal form of the human IgE-Fc(epsilon)3-4 bound to its B cell… · the same entry in another collection · chain H against H, 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 0.97
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 4KI1 · PDBe 4KI1 · UniProt P01854 · UniProt P06734
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