MolNFT v1 · #93066 · protein
Crystal structure of IgE complexed with E2_79, an anti-IgE inhibitor
4GRG · Anti-IgE inhibitor E2_79: “Crystal structure of IgE complexed with E2_79, an anti-IgE inhibitor”. X-ray diffraction, 14 pockets (best druggability 0.56). MolNFT v1 #93066 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4GRG
- Type
- protein
- Length
- 675 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-IgE inhibitor E2_79; Ig epsilon chain C region
- UniProt
- P01854
- Pockets
- 14 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Anti-IgE inhibitor E2_79 | protein | 124 | 45% helix, 0% strand | — |
| C | Ig epsilon chain C region | protein | 214 | 9% helix, 47% strand | P01854 |
| D | Ig epsilon chain C region | protein | 213 | 9% helix, 47% strand | P01854 |
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 152 | 0.56 | 0.81 | 24 | empty |
| 2 | 89 | 0.55 | 0.85 | 19 | empty |
| 3 | 151 | 0.51 | 0.79 | 23 | empty |
| 4 | 82 | 0.46 | 0.81 | 22 | empty |
| 5 | 161 | 0.44 | 0.75 | 25 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1572 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 799 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 786 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4GRG · Crystal structure of IgE complexed with E2_79, an anti-IgE inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P01854 · AlphaFold monomer V2.0 prediction for immunoglobulin heavy constant epsilon (P01854) · a predicted model of the same protein · chain D against A, TM-score 0.94
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 4GRG · PDBe 4GRG · UniProt P01854
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