Research workbench
Fab fragment of antibody against fullerene C60
Analyse Fab fragment of antibody against fullerene C60 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H3H
- Type
- protein
- Length
- 866 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.92
- Source
- Mus musculus
- Molecule
- Anti-fullerene antibody Fab fragment Heavy chain; Anti-fullerene antibody Fab fragment…
- Ligands
- SO4
- Pockets
- 13 · best druggability 0.68
Structure
x-ray diffraction · resolution 1.92 · 3 distinct chains · 8% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anti-fullerene antibody Fab fragment Heavy chain | protein | 222 | 9% helix, 53% strand | — |
| B, D | Anti-fullerene antibody Fab fragment Light chain | protein | 215 | 7% helix, 54% strand | — |
| C | Anti-fullerene antibody Fab fragment Heavy chain | protein | 214 | 7% helix, 54% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 620 | 0.68 | 0.77 | 50 | empty |
| 2 | 558 | 0.65 | 0.76 | 53 | empty |
| 3 | 303 | 0.60 | 0.78 | 36 | empty |
| 4 | 144 | 0.47 | 0.77 | 25 | empty |
| 5 | 151 | 0.45 | 0.76 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1851 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1847 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 398 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6H3H · Fab fragment of antibody against fullerene C60 · the same entry in another collection · chain A against A, 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 6H3H · PDBe 6H3H
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