Research workbench
Unliganded Fab structure of lipid a-specific antibody S55-3
Analyse Unliganded Fab structure of lipid a-specific antibody S55-3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ODS
- Type
- protein
- Length
- 437 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S55-3 Fab (IGG2B) heavy chain
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | S55-3 Fab (IGG2B) heavy chain | protein | 219 | 3% helix, 50% strand | — |
| L | S55-3 Fab (IGG2B) heavy chain | protein | 218 | 6% helix, 52% strand | — |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 738 | 0.67 | 0.75 | 74 | empty |
| 2 | 103 | 0.44 | 0.78 | 21 | empty |
| 3 | 112 | 0.39 | 0.75 | 27 | empty |
| 4 | 91 | 0.33 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- H–L · 2135 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4ODS · Unliganded Fab structure of lipid A-specific antibody S55-3 · 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 4ODS · PDBe 4ODS
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