Research workbench
The cryo-EM structure of hav bound to a neutralizing antibody-F6
Analyse The cryo-EM structure of hav bound to a neutralizing antibody-F6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JHR
- Type
- protein
- Length
- 1,152 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; VP2; VP3; Fab light chain; Fab heavy chain
- Pockets
- 11 · best druggability 0.65
Structure
electron microscopy · 5 distinct chains · 6% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 260 | 11% helix, 29% strand | — |
| B | VP2 | protein | 216 | 9% helix, 38% strand | — |
| C | VP3 | protein | 246 | 5% helix, 33% strand | — |
| D | Fab light chain | protein | 213 | 4% helix, 44% strand | — |
| E | Fab heavy chain | protein | 217 | 1% helix, 46% strand | — |
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 383 | 0.65 | 0.79 | 53 | empty |
| 2 | 243 | 0.59 | 0.80 | 31 | empty |
| 3 | 258 | 0.59 | 0.79 | 30 | empty |
| 4 | 441 | 0.56 | 0.74 | 51 | empty |
| 5 | 131 | 0.43 | 0.76 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–C · 3946 Ų buried · 56 hydrogen bonds · protein-protein
- D–E · 2076 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1680 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1510 Ų buried · 20 hydrogen bonds · protein-protein
- C–E · 896 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6JHR · The cryo-EM structure of HAV bound to a neutralizing antibody-F6 · 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 6JHR · PDBe 6JHR
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