Research workbench
Duck hepatitis B virus capsid mutant R124E_DELTA78-122
Analyse Duck hepatitis B virus capsid mutant R124E_DELTA78-122 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YGI
- Type
- protein
- Length
- 633 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid PROTEIN,CAPSID protein
- UniProt
- P0C6J7
- Pockets
- 7 · best druggability 0.77
Structure
electron microscopy · 5 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, H | Capsid PROTEIN,CAPSID protein | protein | 13 | 0% helix, 0% strand | P0C6J7 |
| A | Capsid PROTEIN,CAPSID protein | protein | 148 | 74% helix, 0% strand | P0C6J7 |
| B | Capsid PROTEIN,CAPSID protein | protein | 151 | 75% helix, 0% strand | P0C6J7 |
| C | Capsid PROTEIN,CAPSID protein | protein | 156 | 69% helix, 0% strand | P0C6J7 |
| D | Capsid PROTEIN,CAPSID protein | protein | 152 | 74% helix, 0% strand | P0C6J7 |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 904 | 0.77 | 0.80 | 80 | empty |
| 2 | 250 | 0.56 | 0.78 | 29 | empty |
| 3 | 161 | 0.55 | 0.81 | 24 | empty |
| 4 | 122 | 0.50 | 0.80 | 25 | empty |
| 5 | 54 | 0.30 | 0.76 | 13 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1243 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 1199 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 739 Ų buried · 9 hydrogen bonds · protein-protein
- H–D · 453 Ų buried · 2 hydrogen bonds · protein-protein
- E–A · 420 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6YGI · Duck hepatitis B virus capsid Mutant R124E_delta78-122 · 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 6YGI · PDBe 6YGI · UniProt P0C6J7
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