MolNFT v1 · #170704 · protein
Duck hepatitis B virus capsid
6YGH · Capsid protein: “Duck hepatitis B virus capsid”. Electron microscopy, 8 pockets (best druggability 0.74). MolNFT v1 #170704 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6YGH
- Type
- protein
- Length
- 790 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein
- UniProt
- P0C6J7
- Pockets
- 8 · best druggability 0.74
Structure
electron microscopy · 5 distinct chains · 66% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, H | Capsid protein | protein | 13 | 0% helix, 0% strand | P0C6J7 |
| A | Capsid protein | protein | 188 | 68% helix, 0% strand | P0C6J7 |
| B | Capsid protein | protein | 192 | 68% helix, 0% strand | P0C6J7 |
| C | Capsid protein | protein | 191 | 71% helix, 0% strand | P0C6J7 |
| D | Capsid protein | protein | 193 | 62% helix, 0% strand | P0C6J7 |
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 560 | 0.74 | 0.82 | 55 | empty |
| 2 | 362 | 0.61 | 0.77 | 31 | empty |
| 3 | 259 | 0.54 | 0.76 | 37 | empty |
| 4 | 90 | 0.53 | 0.84 | 24 | empty |
| 5 | 146 | 0.49 | 0.78 | 26 | empty |
Interfaces
8 interfaces between chains.
- C–D · 2062 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 2053 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 825 Ų buried · 6 hydrogen bonds · protein-protein
- H–D · 511 Ų buried · 3 hydrogen bonds · protein-protein
- E–A · 443 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6YGH · Duck hepatitis B virus capsid · the same entry in another collection · chain E against E, 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 P0C6J7
- Elsewhere: RCSB PDB 6YGH · PDBe 6YGH · UniProt P0C6J7
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