Research workbench
Crystal structure of the omalizumab Fab - crystal form II
Analyse Crystal structure of the omalizumab Fab - crystal form II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TCN
- Type
- protein
- Length
- 863 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Omalizumab Fab
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A | Omalizumab Fab | protein | 217 | 6% helix, 53% strand | — |
| H | Omalizumab Fab | protein | 217 | 7% helix, 51% strand | — |
| B | Omalizumab Fab | protein | 212 | 6% helix, 52% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains L, H, B
- EDO · 1,2-ethanediol · additive · 8 copies · chains L, A, H
- PEG · Di(hydroxyethyl)ether · additive · chains H
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 890 | 0.83 | 0.85 | 95 | empty |
| 2 | 53 | 0.37 | 0.80 | 13 | empty |
| 3 | 85 | 0.37 | 0.76 | 15 | empty |
| 4 | 68 | 0.37 | 0.78 | 16 | empty |
| 5 | 102 | 0.35 | 0.74 | 24 | empty |
Interfaces
5 interfaces between chains.
- L–H · 1796 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1740 Ų buried · 14 hydrogen bonds · protein-protein
- L–A · 616 Ų buried · 7 hydrogen bonds · protein-protein
- H–A · 254 Ų buried · 2 hydrogen bonds · protein-protein
- L–B · 47 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6TCN · Crystal structure of the omalizumab Fab - crystal form II · the same entry in another collection · chain L against L, 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 6TCN · PDBe 6TCN
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