Research workbench
X-ray structure of the birnavirus VP1-VP3 complex
Analyse X-ray structure of the birnavirus VP1-VP3 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZED
- Type
- protein
- Length
- 2,324 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase; Capsid protein VP3
- EC
- 2.7.7.48
- UniProt
- P22173, P05844
- Ligands
- K
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 765 | 47% helix, 14% strand | P22173 |
| B | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 766 | 47% helix, 14% strand | P22173 |
| D | Capsid protein VP3 | protein | 12 | 25% helix, 0% strand | P05844 |
| E, F | Capsid protein VP3 | protein | 8 | 0% helix, 0% strand | P05844 |
Ligands and binding sites
- K · Potassium ion · metal · 6 copies · chains A, B, C
- GOL · Glycerol · additive · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 565 | 0.78 | 0.84 | 53 | empty |
| 2 | 506 | 0.77 | 0.85 | 55 | empty |
| 3 | 224 | 0.70 | 0.86 | 41 | empty |
| 4 | 57 | 0.70 | 0.97 | 19 | empty |
| 5 | 55 | 0.66 | 0.95 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–D · 733 Ų buried · 13 hydrogen bonds · protein-protein
- C–F · 686 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 675 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 629 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 478 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3ZED · X-ray structure of the birnavirus VP1-VP3 complex · 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 P22173
- Every structure of UniProt P05844
- Elsewhere: RCSB PDB 3ZED · PDBe 3ZED · UniProt P22173 · UniProt P05844
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