MolNFT v1 · #102174 · protein
Fab structure of lipid a-specific antibody A6 in complex with lipid a carbohydrate backbone
4ODV · A6 Fab (IGG2B kappa) light chain: “Fab structure of lipid a-specific antibody A6 in complex with lipid a carbohydrate backbone”. X-ray diffraction, 2 ligands (GP1, Z9M), 5 pockets (best druggability 0.55). MolNFT v1 #102174 on…
- PDB
- 4ODV
- Type
- protein
- Length
- 436 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- A6 Fab (IGG2B kappa) light chain; A6 Fab (IGG2B) heavy chain
- Ligands
- GP1, Z9M
- Pockets
- 5 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | A6 Fab (IGG2B kappa) light chain | protein | 214 | 7% helix, 50% strand | — |
| H | A6 Fab (IGG2B) heavy chain | protein | 222 | 4% helix, 55% strand | — |
Ligands and binding sites
- GP1 · 2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose · ligand · chains L, H
- Z9M · 2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose · ligand · chains L, H
- PEG · Di(hydroxyethyl)ether · additive · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 332 | 0.55 | 0.75 | 45 | empty |
| 2 | 174 | 0.50 | 0.78 | 24 | empty |
| 3 | 112 | 0.42 | 0.77 | 23 | empty |
| 4 | 86 | 0.35 | 0.75 | 25 | empty |
| 5 | 74 | 0.30 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- L–H · 2046 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4ODV · Fab Structure of lipid A-specific antibody A6 in complex with lipid A carbohydrate… · 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 4ODV · PDBe 4ODV
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