Research workbench
Structure of omalizumab Fab fragment, crystal form 2
Analyse Structure of omalizumab Fab fragment, crystal form 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X7T
- Type
- protein
- Length
- 880 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Omalizumab-Fab heavy chain; Omalizumab-Fab light chain
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, A | Omalizumab-Fab heavy chain | protein | 222 | 8% helix, 50% strand | — |
| L, B | Omalizumab-Fab light chain | protein | 218 | 6% helix, 55% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains H, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 870 | 0.83 | 0.85 | 88 | empty |
| 2 | 286 | 0.59 | 0.78 | 38 | empty |
| 3 | 455 | 0.58 | 0.74 | 50 | empty |
| 4 | 59 | 0.57 | 0.90 | 21 | empty |
| 5 | 269 | 0.56 | 0.77 | 39 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1934 Ų buried · 18 hydrogen bonds · protein-protein
- H–L · 1888 Ų buried · 16 hydrogen bonds · protein-protein
- L–B · 653 Ų buried · 10 hydrogen bonds · protein-protein
- H–B · 226 Ų buried · 1 hydrogen bond · protein-protein
- L–A · 39 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4X7T · Structure of Omalizumab Fab fragment, crystal form 2 · the same entry in another collection · chain H against H, 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
- Elsewhere: RCSB PDB 4X7T · PDBe 4X7T
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