MolNFT v1 · #187515 · protein
IgE-Fc in complex with omalizumab variant C02
7SHU · Omalizumab variant C02 vh: “IgE-Fc in complex with omalizumab variant C02”. X-ray diffraction, 4 ligands (NAG, BMA, MAN), 11 pockets (best druggability 0.66). MolNFT v1 #187515 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7SHU
- Type
- protein
- Length
- 838 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Omalizumab variant C02 vh; Omalizumab variant C02 vl; Immunoglobulin heavy constant…
- UniProt
- P01854
- Ligands
- NAG, BMA, MAN, PO4
- Pockets
- 11 · best druggability 0.66
Structure
x-ray diffraction · 6 distinct chains · 6% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Omalizumab variant C02 vh | protein | 120 | 3% helix, 59% strand | — |
| F | Omalizumab variant C02 vl | protein | 112 | 3% helix, 49% strand | — |
| B | Immunoglobulin heavy constant epsilon | protein | 203 | 10% helix, 44% strand | P01854 |
| C | Omalizumab variant C02 vh | protein | 122 | 2% helix, 55% strand | — |
| D | Omalizumab variant C02 vl | protein | 115 | 3% helix, 48% strand | — |
| A | Immunoglobulin heavy constant epsilon | protein | 166 | 13% helix, 37% strand | P01854 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, C, E
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains B
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- PO4 · Phosphate ion · ion · chains E, F, B
- EDO · 1,2-ethanediol · additive · chains E, F
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 | 764 | 0.66 | 0.74 | 83 | empty |
| 2 | 367 | 0.56 | 0.74 | 45 | PO4 |
| 3 | 168 | 0.54 | 0.80 | 29 | empty |
| 4 | 112 | 0.43 | 0.77 | 21 | empty |
| 5 | 63 | 0.41 | 0.80 | 12 | empty |
Interfaces
8 interfaces between chains.
- C–D · 932 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 916 Ų buried · 11 hydrogen bonds · protein-protein
- C–A · 549 Ų buried · 8 hydrogen bonds · protein-protein
- E–B · 538 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 523 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
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 7SHU · PDBe 7SHU · UniProt P01854
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