Research workbench
Crystal structure of decameric bfdv capsid protein
Analyse Crystal structure of decameric bfdv capsid protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J09
- Type
- protein
- Length
- 1,698 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beak and feather disease virus capsid protein
- UniProt
- A0A023R6W2
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beak and feather disease virus capsid protein | protein | 171 | 10% helix, 46% strand | A0A023R6W2 |
| B, C, H, I | Beak and feather disease virus capsid protein | protein | 169 | 10% helix, 47% strand | A0A023R6W2 |
| D | Beak and feather disease virus capsid protein | protein | 171 | 12% helix, 47% strand | A0A023R6W2 |
| E, F, G, J | Beak and feather disease virus capsid protein | protein | 170 | 11% helix, 47% strand | A0A023R6W2 |
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 812 | 0.79 | 0.82 | 116 | empty |
| 2 | 771 | 0.78 | 0.82 | 103 | empty |
| 3 | 690 | 0.78 | 0.83 | 80 | empty |
| 4 | 707 | 0.77 | 0.82 | 89 | empty |
| 5 | 399 | 0.73 | 0.84 | 54 | empty |
Interfaces
20 interfaces between chains.
- C–J · 910 Ų buried · 19 hydrogen bonds · protein-protein
- B–F · 903 Ų buried · 20 hydrogen bonds · protein-protein
- G–J · 903 Ų buried · 19 hydrogen bonds · protein-protein
- A–G · 898 Ų buried · 17 hydrogen bonds · protein-protein
- H–I · 886 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5J09 · Crystal structure of decameric BFDV Capsid Protein · 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 A0A023R6W2
- Elsewhere: RCSB PDB 5J09 · PDBe 5J09 · UniProt A0A023R6W2
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