Research workbench
Crystal structure of an anti-HBV E-antigen monoclonal Fab fragment (E6), unbound
Analyse Crystal structure of an anti-HBV E-antigen monoclonal Fab fragment (E6), unbound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V6F
- Type
- protein
- Length
- 1,733 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab E6 heavy chain; Fab E6 light chain
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab E6 heavy chain | protein | 218 | 6% helix, 53% strand | — |
| B, D, F, L | Fab E6 light chain | protein | 219 | 6% helix, 54% strand | — |
| C, E | Fab E6 heavy chain | protein | 212 | 4% helix, 53% strand | — |
| H | Fab E6 heavy chain | protein | 215 | 6% helix, 51% strand | — |
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 925 | 0.69 | 0.75 | 92 | empty |
| 2 | 547 | 0.61 | 0.75 | 76 | empty |
| 3 | 184 | 0.60 | 0.82 | 24 | empty |
| 4 | 167 | 0.57 | 0.81 | 24 | empty |
| 5 | 364 | 0.56 | 0.75 | 45 | empty |
Interfaces
12 interfaces between chains.
- C–D · 1889 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1882 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1835 Ų buried · 18 hydrogen bonds · protein-protein
- H–L · 1830 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 327 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 3V6F · Crystal Structure of an anti-HBV e-antigen monoclonal Fab fragment (e6), unbound · 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 3V6F · PDBe 3V6F
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