Research workbench
Crystal structure of the omalizumab Fab - crystal form I
Analyse Crystal structure of the omalizumab Fab - crystal form I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TCM
- Type
- protein
- Length
- 439 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.85
- Source
- Homo sapiens
- Molecule
- Omalizumab Fab
- Ligands
- PO4
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · resolution 1.85 · 2 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Omalizumab Fab | protein | 217 | 6% helix, 53% strand | — |
| H | Omalizumab Fab | protein | 222 | 9% helix, 50% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains L, H
- GOL · Glycerol · additive · 8 copies · chains L, H
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 577 | 0.60 | 0.73 | 69 | GOL |
| 2 | 50 | 0.52 | 0.89 | 21 | GOL |
| 3 | 111 | 0.38 | 0.74 | 25 | empty |
| 4 | 66 | 0.27 | 0.72 | 15 | empty |
Interfaces
1 interface between chains.
- L–H · 1893 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6TCM · Crystal structure of the omalizumab Fab - crystal form I · 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 6TCM · PDBe 6TCM
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