Research workbench
Crystal structure of the dutpase of white spot syndrome virus in the apo state
Analyse Crystal structure of the dutpase of white spot syndrome virus in the apo state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y5O
- Type
- protein
- Length
- 886 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- WSV112
- UniProt
- Q77J78
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, F | WSV112 | protein | 148 | 5% helix, 45% strand | Q77J78 |
| B, E | WSV112 | protein | 147 | 5% helix, 45% strand | Q77J78 |
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 346 | 0.85 | 0.95 | 44 | empty |
| 2 | 350 | 0.85 | 0.94 | 45 | empty |
| 3 | 156 | 0.50 | 0.78 | 24 | empty |
| 4 | 175 | 0.50 | 0.77 | 27 | empty |
| 5 | 177 | 0.50 | 0.77 | 25 | empty |
Interfaces
7 interfaces between chains.
- A–C · 1651 Ų buried · 28 hydrogen bonds · protein-protein
- D–F · 1635 Ų buried · 33 hydrogen bonds · protein-protein
- D–E · 1583 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1564 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1501 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 5Y5O · Crystal structure of the dUTPase of white spot syndrome virus in the apo state · 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 Q77J78
- Elsewhere: RCSB PDB 5Y5O · PDBe 5Y5O · UniProt Q77J78
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