Research workbench
Cryo-EM structure for hepatitis a virus complexed with Fab
Analyse Cryo-EM structure for hepatitis a virus complexed with Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WTH
- Type
- protein
- Length
- 1,152 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyprotein; VP2; VP3; Fab light chain; Fab heavy chain
- Pockets
- 14 · best druggability 0.71
Structure
electron microscopy · 5 distinct chains · 8% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyprotein | protein | 260 | 12% helix, 28% strand | — |
| B | VP2 | protein | 217 | 9% helix, 39% strand | — |
| C | VP3 | protein | 246 | 9% helix, 31% strand | — |
| D | Fab light chain | protein | 212 | 6% helix, 47% strand | — |
| E | Fab heavy chain | protein | 217 | 4% helix, 53% strand | — |
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.71 | 0.81 | 63 | empty |
| 2 | 426 | 0.65 | 0.78 | 50 | empty |
| 3 | 452 | 0.61 | 0.76 | 49 | empty |
| 4 | 192 | 0.46 | 0.75 | 33 | empty |
| 5 | 131 | 0.44 | 0.76 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–C · 3830 Ų buried · 51 hydrogen bonds · protein-protein
- D–E · 1984 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1466 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1370 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 266 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5WTH · Cryo-EM structure for Hepatitis A virus complexed with FAB · 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 5WTH · PDBe 5WTH
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.