Research workbench
Fab structure of lipid a-specific antibody S1-15 in complex with lipid a carbohydrate backbone
Analyse Fab structure of lipid a-specific antibody S1-15 in complex with lipid a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ODT
- Type
- protein
- Length
- 440 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S1-15 Fab (IGG2B) heavy chain; S1-15 Fab (IGG2B kappa) light chain
- Ligands
- GP1, Z9M
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | S1-15 Fab (IGG2B) heavy chain | protein | 226 | 8% helix, 50% strand | — |
| L | S1-15 Fab (IGG2B kappa) light chain | protein | 214 | 7% helix, 50% strand | — |
Ligands and binding sites
- GP1 · 2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose · ligand · chains H
- Z9M · 2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose · ligand · chains H
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · 4 copies · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 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 | 0.62 | 0.74 | 64 | PG0 |
| 2 | 185 | 0.56 | 0.80 | 28 | empty |
| 3 | 64 | 0.45 | 0.83 | 20 | empty |
| 4 | 104 | 0.36 | 0.74 | 19 | empty |
| 5 | 82 | 0.33 | 0.74 | 21 | PG0 |
Interfaces
1 interface between chains.
- H–L · 1990 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4ODT · Fab Structure of lipid A-specific antibody S1-15 in complex with lipid A carbohydrate… · 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 4ODT · PDBe 4ODT
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