MolNFT v1 · #166464 · protein
Complex of IgE and ligelizumab
6UQR: “Complex of IgE and ligelizumab”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 11 pockets (best druggability 0.64). MolNFT v1 #166464 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6UQR
- Type
- protein
- Length
- 869 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ligelizumab; IgE
- UniProt
- P01854
- Ligands
- NAG, MAN, BMA
- Pockets
- 11 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ligelizumab | protein | 224 | 1% helix, 47% strand | — |
| B, D | IgE | protein | 212 | 9% helix, 46% strand | P01854 |
| C | Ligelizumab | protein | 221 | 1% helix, 44% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, D
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains B
- 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
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.64 | 0.91 | 25 | empty |
| 2 | 453 | 0.63 | 0.77 | 47 | empty |
| 3 | 406 | 0.60 | 0.76 | 40 | empty |
| 4 | 267 | 0.50 | 0.74 | 39 | empty |
| 5 | 60 | 0.49 | 0.85 | 18 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1284 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 780 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 623 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 205 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 117 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6UQR · Complex of IgE and Ligelizumab · the same entry in another collection · chain A against A, TM-score 1.00
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 6UQR · PDBe 6UQR · UniProt P01854
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.