Research workbench
Crystal structure of envelope protein VP28 from white spot syndrome virus (wssv)
Analyse Crystal structure of envelope protein VP28 from white spot syndrome virus (wssv) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ED6
- Type
- protein
- Length
- 2,040 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 25KDA structural protein VP25
- UniProt
- Q9ICB7
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | 25KDA structural protein VP25 | protein | 170 | 14% helix, 44% strand | Q9ICB7 |
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 893 | 0.86 | 0.88 | 98 | empty |
| 2 | 928 | 0.86 | 0.87 | 104 | empty |
| 3 | 785 | 0.84 | 0.87 | 105 | empty |
| 4 | 589 | 0.83 | 0.88 | 62 | empty |
| 5 | 189 | 0.80 | 0.95 | 28 | empty |
Interfaces
18 interfaces between chains.
- J–K · 1226 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1223 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1214 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 1203 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1203 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 2ED6 · Crystal Structure of Envelope Protein VP28 from White Spot Syndrome Virus (WSSV) · 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 Q9ICB7
- Elsewhere: RCSB PDB 2ED6 · PDBe 2ED6 · UniProt Q9ICB7
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