MolNFT v1 · #144495 · protein
Cryo-EM structure of hepatitis B virus T=4 capsid in complex with the fluorescent allosteric modulator hap-tamra
6BVF · Capsid protein: “Cryo-EM structure of hepatitis B virus T=4 capsid in complex with the fluorescent allosteric modulator…”. Electron microscopy, 1 ligand (E9D), 6 pockets (best druggability 0.70). MolNFT v1 #144495 on GenesisL1: 3D…
- PDB
- 6BVF
- Type
- protein
- Length
- 568 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein
- UniProt
- P03147
- Ligands
- E9D
- Pockets
- 6 · best druggability 0.70
Structure
electron microscopy · 1 distinct chain · 65% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Capsid protein | protein | 142 | 65% helix, 0% strand | P03147 |
Ligands and binding sites
- E9D · Heteroaryldihydropyrimidine tetramethylrodamine · ligand · 2 copies · chains B, C
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 | 300 | 0.70 | 0.83 | 28 | E9D |
| 2 | 182 | 0.59 | 0.81 | 34 | empty |
| 3 | 86 | 0.50 | 0.83 | 19 | empty |
| 4 | 70 | 0.49 | 0.83 | 16 | empty |
| 5 | 58 | 0.43 | 0.82 | 17 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1945 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1926 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 512 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6BVF · Cryo-EM Structure of Hepatitis B virus T=4 capsid in complex with the fluorescent… · 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 6BVF · PDBe 6BVF · UniProt P03147
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