MolNFT v1 · #140280 · protein
Crystal structure of the dutpase of white spot syndrome virus in the apo state
5Y5O · WSV112: “Crystal structure of the dutpase of white spot syndrome virus in the apo state”. X-ray diffraction, 8 pockets (best druggability 0.85). MolNFT v1 #140280 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- 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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