Research workbench
Cryo-EM structure of hepatitis B virus T=4 capsid in complex with the antiviral molecule DBT1
Analyse Cryo-EM structure of hepatitis B virus T=4 capsid in complex with the antiviral… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WFS
- Type
- protein
- Length
- 568 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein
- UniProt
- P03147
- Ligands
- U0A
- Pockets
- 6 · best druggability 0.70
Structure
electron microscopy · 1 distinct chain · 53% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Capsid protein | protein | 142 | 53% helix, 0% strand | P03147 |
Ligands and binding sites
- U0A · 11-oxo-N-[2-(4-sulfamoylphenyl)ethyl]-10,11-dihydrodibenzo[b,f][1,4]thiazepine-8-carboxamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 252 | 0.70 | 0.85 | 33 | U0A |
| 2 | 92 | 0.62 | 0.88 | 22 | empty |
| 3 | 107 | 0.52 | 0.82 | 16 | empty |
| 4 | 112 | 0.49 | 0.80 | 14 | empty |
| 5 | 61 | 0.44 | 0.82 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2079 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1775 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 593 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6WFS · Cryo-EM Structure of Hepatitis B virus T=4 capsid in complex with the antiviral molecule… · 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
- Every structure of UniProt P03147
- Elsewhere: RCSB PDB 6WFS · PDBe 6WFS · UniProt P03147
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