Research workbench
Crystal structure of the omalizumab Fab SER81ARG, GLN83ARG and LEU158PRO light chain mutant
Analyse Crystal structure of the omalizumab Fab SER81ARG, GLN83ARG and LEU158PRO light… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TCR
- Type
- protein
- Length
- 428 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Omalizumab Fab SER81ARG, GLN83ARG and LEU158PRO light chain mutant
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Omalizumab Fab SER81ARG, GLN83ARG and LEU158PRO light chain mutant | protein | 212 | 8% helix, 54% strand | — |
| L | Omalizumab Fab SER81ARG, GLN83ARG and LEU158PRO light chain mutant | protein | 216 | 6% helix, 53% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 8 copies · chains H, L
- PEG · Di(hydroxyethyl)ether · additive · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 594 | 0.61 | 0.73 | 56 | EDO |
| 2 | 64 | 0.53 | 0.87 | 22 | empty |
| 3 | 54 | 0.34 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- H–L · 1787 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6TCR · Crystal structure of the omalizumab Fab Ser81Arg, Gln83Arg and Leu158Pro light chain… · 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 6TCR · PDBe 6TCR
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