Research workbench
Crystal structure of HBV capsid mutant dimer (oxy form), strain adyw
Analyse Crystal structure of HBV capsid mutant dimer (oxy form), strain adyw in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KXS
- Type
- protein
- Length
- 850 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein
- UniProt
- P03147
- Pockets
- 9 · best druggability 0.58
Structure
x-ray diffraction · 4 distinct chains · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F, C, B | Capsid protein | protein | 142 | 70% helix, 0% strand | P03147 |
| E | Capsid protein | protein | 143 | 69% helix, 0% strand | P03147 |
| D | Capsid protein | protein | 141 | 69% helix, 0% strand | P03147 |
| A | Capsid protein | protein | 140 | 67% helix, 0% strand | P03147 |
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.58 | 0.86 | 26 | empty |
| 2 | 96 | 0.56 | 0.85 | 21 | empty |
| 3 | 100 | 0.55 | 0.84 | 21 | empty |
| 4 | 112 | 0.50 | 0.81 | 21 | empty |
| 5 | 75 | 0.49 | 0.83 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2017 Ų buried · 16 hydrogen bonds · protein-protein
- F–E · 1969 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1934 Ų buried · 17 hydrogen bonds · protein-protein
- C–B · 488 Ų buried · 1 hydrogen bond · protein-protein
- E–D · 456 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3KXS · Crystal structure of HBV capsid mutant dimer (oxy form), strain adyw · the same entry in another collection · chain F against F, 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 3KXS · PDBe 3KXS · UniProt P03147
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