Research workbench
Crystal structure of the LT1009 (sonepcizumab) antibody Fab fragment in complex with sphingosine-1-phosphate
Analyse Crystal structure of the LT1009 (sonepcizumab) antibody Fab fragment in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3I9G
- Type
- protein
- Length
- 435 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sonepcizumab antibody Fab fragment, heavy chain; Sonepcizumab antibody Fab fragment…
- Ligands
- S1P, MG, CA
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Sonepcizumab antibody Fab fragment, heavy chain | protein | 222 | 7% helix, 50% strand | — |
| L | Sonepcizumab antibody Fab fragment, light chain | protein | 213 | 6% helix, 50% strand | — |
Ligands and binding sites
- S1P · (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate · ligand · chains H, L
- MG · Magnesium ion · metal · 5 copies · chains L
- CA · Calcium ion · metal · 2 copies · 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 | 132 | 0.56 | 0.82 | 23 | S1P |
| 2 | 279 | 0.51 | 0.74 | 38 | empty |
| 3 | 150 | 0.43 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- H–L · 1820 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3I9G · Crystal structure of the LT1009 (SONEPCIZUMAB) antibody Fab fragment in complex with… · 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 3I9G · PDBe 3I9G
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