Research workbench
Unliganded Fab structure of lipid a-specific antibody S1-15
Analyse Unliganded Fab structure of lipid a-specific antibody S1-15 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ODU
- Type
- protein
- Length
- 867 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S1-15 Fab (IGG2B kappa) light chain; S1-15 Fab (IGG2B) heavy chain
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, B | S1-15 Fab (IGG2B kappa) light chain | protein | 212 | 6% helix, 52% strand | — |
| H | S1-15 Fab (IGG2B) heavy chain | protein | 224 | 11% helix, 49% strand | — |
| A | S1-15 Fab (IGG2B) heavy chain | protein | 219 | 11% helix, 51% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains H, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1081 | 0.76 | 0.79 | 118 | SO4 |
| 2 | 818 | 0.73 | 0.78 | 83 | empty |
| 3 | 64 | 0.57 | 0.89 | 17 | empty |
| 4 | 210 | 0.56 | 0.79 | 42 | SO4 |
| 5 | 146 | 0.48 | 0.77 | 21 | empty |
Interfaces
5 interfaces between chains.
- L–H · 1942 Ų buried · 14 hydrogen bonds · protein-protein
- B–A · 1877 Ų buried · 14 hydrogen bonds · protein-protein
- H–A · 1381 Ų buried · 22 hydrogen bonds · protein-protein
- L–A · 30 Ų buried · 0 hydrogen bonds · protein-protein
- H–B · 22 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4ODU · Unliganded Fab structure of lipid A-specific antibody S1-15 · 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 4ODU · PDBe 4ODU
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