MolNFT v1 · #187517 · protein
IgE-Fc in complex with omalizumab scfv
7SHY · Omalizumab vh: “IgE-Fc in complex with omalizumab scfv”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.69). MolNFT v1 #187517 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7SHY
- Type
- protein
- Length
- 1,771 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Omalizumab vh; Omalizumab vl; IgE Fc
- UniProt
- P01854
- Ligands
- NAG, MAN, BMA, FUC
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 9 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I, K | Omalizumab vh | protein | 120 | 5% helix, 58% strand | — |
| C, E | Omalizumab vh | protein | 121 | 5% helix, 57% strand | — |
| J | Omalizumab vl | protein | 115 | 3% helix, 50% strand | — |
| L | Omalizumab vl | protein | 113 | 3% helix, 51% strand | — |
| D | Omalizumab vl | protein | 114 | 3% helix, 51% strand | — |
| A, H | IgE Fc | protein | 208 | 10% helix, 46% strand | P01854 |
| G | IgE Fc | protein | 209 | 10% helix, 48% strand | P01854 |
| F | Omalizumab vl | protein | 112 | 3% helix, 52% strand | — |
| B | IgE Fc | protein | 210 | 8% helix, 47% strand | P01854 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, G, H, B, F
- MAN · alpha-D-mannopyranose · sugar · 10 copies · chains A, G, H, B
- BMA · beta-D-mannopyranose · sugar · 5 copies · chains A, G, H, B
- FUC · alpha-L-fucopyranose · sugar · chains A
- GOL · Glycerol · additive · chains C, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 297 | 0.69 | 0.83 | 34 | empty |
| 2 | 50 | 0.63 | 0.94 | 17 | empty |
| 3 | 286 | 0.53 | 0.75 | 42 | empty |
| 4 | 262 | 0.52 | 0.75 | 36 | empty |
| 5 | 260 | 0.50 | 0.74 | 38 | empty |
Interfaces
21 interfaces between chains.
- A–B · 1265 Ų buried · 7 hydrogen bonds · protein-protein
- I–J · 960 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 931 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 914 Ų buried · 10 hydrogen bonds · protein-protein
- K–L · 910 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 6 glycan (disulfide, N-glycosylation, O-glycosylation).
Compared structures
- 7SHY · IgE-Fc in complex with omalizumab scFv · the same entry in another collection · chain B against B, 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 7SHY · PDBe 7SHY · UniProt P01854
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